CN106701979A - Kit used for mycobacterium tuberculosis typing SNP site and application thereof - Google Patents

Kit used for mycobacterium tuberculosis typing SNP site and application thereof Download PDF

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CN106701979A
CN106701979A CN201710063939.6A CN201710063939A CN106701979A CN 106701979 A CN106701979 A CN 106701979A CN 201710063939 A CN201710063939 A CN 201710063939A CN 106701979 A CN106701979 A CN 106701979A
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nucleotides
mycobacterium tuberculosis
snp site
tuberculosis chromosome
chromosome
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李卫民
陈海霞
贾俊楠
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Beijing Tuberculosis and Thoracic Tumor Research Institute
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Beijing Tuberculosis and Thoracic Tumor Research Institute
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    • C12Q2600/156—Polymorphic or mutational markers

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Abstract

The invention relates to a kit used for a mycobacterium tuberculosis typing SNP site and application thereof. Specifically, the invention provides a kit for detecting a mycobacterium tuberculosis SNP site, corresponding application and a method for carrying out typing and evolution analysis on mycobacterium tuberculosis. The kit, application and method relate to an SNP set comprising SNP sites 1-285, the mycobacterium tuberculosis can be subdivided into 7 large lineages, 67 second lineages, a M.bovis lineage and a sub lineage thereof M.bovis1 by virtue of the SNP set, and the resolution ratio of SNP in the mycobacterium tuberculosis is obviously improved.

Description

A kind of kit and its application for typing of Mycobacterium tuberculosis SNP site
Technical field
The present invention relates to SNP marker field, typing of Mycobacterium tuberculosis SNP to be used in particular to one kind The kit of point and its application.
Background technology
It, with one of human history disease most long, is also the whole world by single cause that tuberculosis (tuberculosis, TB) is Germ causes the most disease of death toll, has become global great public health problem, preventing and controlling accepting a heavy burden lungy And road is remote.
Mycobacterium tuberculosis (M.tuberculosis), is commonly called as tubercle bacillus, is to cause pathogen lungy.Global model The mycobacterium tuberculosis for enclosing interior prevalence is classified largely into 6 big pedigrees and a small number of Asia pedigrees.The mycobacterium tuberculosis of different pedigrees exists The aspects such as virulence, pathogenicity, vaccine potency change and the resistance to the action of a drug have larger difference, therefore, it is necessary to mycobacterium tuberculosis Pedigree is finely divided.
At present, the classifying method of mycobacterium tuberculosis mainly has：Sequence polymorphism (LSP) parting long, Spoligotyping Parting and SNP (SNP) parting.LSP partings are lacked based on difference section (RD) in mycobacterium tuberculosis gene group The mycobacterium tuberculosis pedigree authentication method for losing and setting up, the method is simple to operate, is completed by only needing regular-PCR, as a result easily Interpretation, but mycobacterium tuberculosis can only be divided into 6 big pedigrees and 15 sub- pedigrees by the method, and resolution capability is not high. Spoligotyping partings are by detecting the different interval sequence on mycobacterium tuberculosis chromosome between DR sequences so as to reality The parting of existing mycobacterium tuberculosis, the classifying method there is also the low defect of resolution ratio.
SNP typing methods are based on being made a variation by single nucleotide acid in genomic level genomic dna sequence can be caused polymorphic Property, from whole genome sequence, its advantage is that have resolution ratio higher to SNP, overcomes the homologous different of other classifying methods The shortcoming of matter, and SNP more meets the evolution laws of mycobacterium tuberculosis.At present, foreign study person has screened SNP site work It is parting target, such as Francesc Coll researchs find that 62 SNP sites can have mycobacterium tuberculosis altogether and are divided into 55 Mycobacterium tuberculosis is divided into 10 sub- pedigrees by individual sub- pedigree, Homolka C etc. with 71 SNP sites, but the country is not sent out Existing a set of ripe SNP classification targets are applied in the practice of prevention and control in mycobacterium tuberculosis.Therefore based on tuberculosis point Branch bacillus whole genome sequence data, finding and filter out a collection of representative SNP site contributes to tuberculosis branch bar Bacterium is divided into more Asia pedigrees, improves its resolution capability.
In view of this, it is special to propose the present invention.
The content of the invention
The first object of the present invention is to provide a kind of kit for detecting mycobacterium tuberculosis SNP site, the kit Including for detecting reagent or component that the SNP of mycobacterium tuberculosis gathers.Mentioned reagent box can be to mycobacterium tuberculosis SNP set is detected, so as to mycobacterium tuberculosis is subdivided into different subtype, resolution of the raising to mycobacterium tuberculosis pedigree Ability.
The second object of the present invention is the parting or evolutionary analysis for providing a kind of mentioned reagent box in mycobacterium tuberculosis In application.Above-mentioned application can improve the accuracy of typing of Mycobacterium tuberculosis or evolutionary analysis.
The third object of the present invention is to provide a kind of mentioned reagent box preparing for tuberculosis infection pathogen hypotype Application in the diagnostic products of judgement.
The fourth object of the present invention is to provide a kind of method that parting or evolutionary analysis are carried out to mycobacterium tuberculosis, institute SNP set of the method using mentioned reagent box to mycobacterium tuberculosis is stated to detect.
In order to realize above-mentioned purpose of the invention, spy uses following technical scheme：
The present invention provides a kind of kit for detecting mycobacterium tuberculosis SNP site, and the kit is included for examining The reagent and/or component of SNP set are surveyed, the SNP set includes following one or more SNP sites, the thing of the SNP site Reason position is that the whole genome sequence based on Mycobacterium tuberculosis H37Rv compares what is determined, the Mycobacterium tuberculosis H37Rv The Accesion Number of whole genome sequence are NC_000962.3：
SNP site 1：The 107791st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 2：The 108136th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 3：The 108181st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 4：The 109040th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 5：The 110395th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 6：The 111848th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 7：The 112333rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 8：The 112490th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 9：The 112734th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 10：The 113139th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 11：The 114695th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 12：The 116225th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 13：The 154049th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 14：The 200152nd on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 15：The 200377th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 16：The 200695th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 17：The 201894th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 18：The 204424th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 19：The 204502nd on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 20：The 207077th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 21：The 207590th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 22：The 208297th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 23：The 258921st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 24：The 259689th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 25：The 301341st on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 26：The 392506th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 27：The 451896th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 28：The 452064th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 29：The 500533rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 30：The 501001st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 31：The 516658th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 32：The 580011st on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 33：The 643386th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 34：The 643751st on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 35：The 644442nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 36：The 644475th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 37：The 646051st on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 38：The 646166th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 39：The 646246th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 40：The 732555th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 41：The 738045th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 42：The 752017th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 43：The 752049th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 44：The 770391st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 45：The 962104th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 46：The 962136th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 47：The 1061309th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 48：The 1129169th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 49：The 1143318th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 50：The 1149132nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 51：The 1149551st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 52：The 1150494th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 53：The 1219669th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 54：The 1219828th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 55：The 1225203rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 56：The 1228121st on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 57：The 1235550th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 58：The 1271192nd on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 59：The 1310360th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 60：The 1324571st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 61：The 1324730th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 62：The 1324997th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 63：The 1325171st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 64：The 1326802nd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 65：The 1347179th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 66：The 1377574th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 67：The 1378731st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 68：The 1386928th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 69：The 1386970th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 70：The 1421046th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 71：The 1421115th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 72：The 1421314th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 73：The 1460672nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 74：The 1486653rd on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 75：The 1494800th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 76：The 1495332nd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 77：The 1501474th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 78：The 1502126th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 79：The 1502348th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 80：The 1505476th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 81：The 1505812nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 82：The 1510163rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 83：The 1581733rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 84：The 1586540th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 85：The 1587020th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 86：The 1588462nd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 87：The 1597411st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 88：The 1656977th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 89：The 1658036th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 90：The 1706040th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 91：The 1719328th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 92：The 1719685th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 93：The 1719829th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 94：The 1776441st on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 95：The 1790486th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 96：The 1791511st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 97：The 1793509th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 98：The 1849198th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 99：The 1850089th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 100：The 1851055th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 101：The 1867845th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 102：The 1919743rd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 103：The 1919952nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 104：The 2066477th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 105：The 2066478th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 106：The 2067686th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 107：The 2095241st on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 108：The 2095536th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 109：The 2183228th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 110：The 2192357th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 111：The 2192591st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 112：The 2202589th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 113：The 2202946th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 114：The 2283874th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 115：The 2294813rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 116：The 2295025th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 117：The 2295037th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 118：The 2295046th on mycobacterium tuberculosis chromosome, its nucleotides is T/A；
SNP site 119：The 2295050th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 120：The 2296751st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 121：The 2298201st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 122：The 2300672nd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 123：The 2300950th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 124：The 2303765th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 125：The 2304076th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 126：The 2329272nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 127：The 2329474th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 128：The 2371795th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 129：The 2371796th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 130：The 2462421st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 131：The 2496838th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 132：The 2505093rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 133：The 2512762nd on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 134：The 2514875th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 135：The 2527686th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 136：The 2547004th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 137：The 2547251st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 138：The 2549266th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 139：The 2549313rd on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 140：The 2549735th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 141：The 2610132nd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 142：The 2610354th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 143：The 2654653rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 144：The 2654706th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 145：The 2672399th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 146：The 2672617th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 147：The 2672916th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 148：The 2673609th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 149：The 2673711st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 150：The 2673858th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 151：The 2681585th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 152：The 2682603rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 153：The 2775550th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 154：The 2789351st on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 155：The 2789808th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 156：The 2789851st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 157：The 2790588th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 158：The 2810392nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 159：The 2810826th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 160：The 2817168th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 161：The 2818256th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 162：The 2859840th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 163：The 2860223rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 164：The 2860313rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 165：The 2872966th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 166：The 2884007th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 167：The 2996922nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 168：The 2997335th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 169：The 3012844th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 170：The 3016914th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 171：The 3016953rd on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 172：The 3017144th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 173：The 3017286th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 174：The 3050372nd on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 175：The 3051081st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 176：The 3118829th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 177：The 3118986th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 178：The 3151823rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 179：The 3152267th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 180：The 3152431st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 181：The 3169022nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 182：The 3194244th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 183：The 3219800th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 184：The 3285955th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 185：The 3286799th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 186：The 3332286th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 187：The 3332665th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 188：The 3336871st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 189：The 3401962nd on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 190：The 3402521st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 191：The 3423423rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 192：The 3423655th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 193：The 3424459th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 194：The 3424865th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 195：The 3453393rd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 196：The 3471148th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 197：The 3536291st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 198：The 3536836th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 199：The 3537013rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 200：The 3606624th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 201：The 3612568th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 202：The 3626906th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 203：The 3651143rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 204：The 3664476th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 205：The 3722442nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 206：The 3786035th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 207：The 3786186th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 208：The 3817476th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 209：The 3817994th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 210：The 3913600th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 211：The 3921273rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 212：The 3959715th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 213：The 3973331st on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 214：The 3979502nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 215：The 3980169th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 216：The 3980398th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 217：The 3981350th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 218：The 3981601st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 219：The 3984549th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 220：The 3985105th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 221：The 3996273rd on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 222：The 3996826th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 223：The 4016684th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 224：The 4030438th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 225：The 4054217th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 226：The 4054902nd on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 227：The 4056097th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 228：The 4056172nd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 229：The 4070666th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 230：The 4090261st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 231：The 4090846th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 232：The 4092848th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 233：The 4095906th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 234：The 4125161st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 235：The 4139309th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 236：The 4168881st on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 237：The 4168949th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 238：The 4201713rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 239：The 4243424th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 240：The 4243509th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 241：The 4243638th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 242：The 4244433rd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 243：The 4244598th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 244：The 4244813rd on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 245：The 4245203rd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 246：The 4245233rd on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 247：The 4245325th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 248：The 4246500th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 249：The 4267450th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 250：The 4267825th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 251：The 4268036th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 252：The 4268751st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 253：The 4273752nd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 254：The 4274020th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 255：The 4327554th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 256：The 4340528th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 257：The 4340731st on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 258：The 4343857th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 259：The 4344236th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 260：The 4345214th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 261：The 4345215th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 262：The 4345598th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 263：The 4347515th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 264：The 4347938th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 265：The 4348596th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 266：The 4349307th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 267：The 4354191st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 268：The 4355319th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 269：The 4355324th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 270：The 4355393rd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 271：The 4355616th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 272：The 4362057th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 273：The 4362473rd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 274：The 4362562nd on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 275：The 4362656th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 276：The 4362746th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 277：The 4363247th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 278：The 4363345th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 279：The 4396673rd on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 280：The 4397307th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 281：The 4398213rd on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 282：The 4398910th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 283：The 4399563rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 284：The 4399600th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 285：The 4400036th on mycobacterium tuberculosis chromosome, its nucleotides is G/C.
Mentioned reagent box of the present invention can be to detecting including the SNP set selected from SNP site 1~285.Institute of the present invention It is acquisition of comparing on the basis of 2372 full-length genome data of mycobacterium tuberculosis to state SNP site 1~285, and Build after the chadogram of mycobacterium tuberculosis by set Fst coefficients filter out can most represent on mycobacterium tuberculosis chadogram it is every The SNP site of one branch and further filter out key gene same sense mutation and obtain SNP set.Therefore, above-mentioned SNP Site admirably characterizes the Pedigree information of mycobacterium tuberculosis and the abrupt information of key gene.Kit of the present invention The above-mentioned SNP site of mycobacterium tuberculosis can be detected, there is provided above- mentioned information, parting to mycobacterium tuberculosis or entered Change analysis significant.
In some embodiments, above-mentioned SNP gathers includes 50~285 above-mentioned SNP sites, or 100~285 above-mentioned SNP site, or 200~285 above-mentioned SNP sites, or 250~285 above-mentioned SNP sites.
The number of the above-mentioned implementation method of present invention SNP site included in gathering SNP is carried out preferably, by preferred SNP set preferably can carry out parting and evolutionary analysis to mycobacterium tuberculosis.
In some embodiments, above-mentioned SNP set includes 285 above-mentioned SNP sites.
The present invention is used to screen the data sample of SNP site from 2372 whole genome sequences of mycobacterium tuberculosis, The most of M. tuberculosis strains for having found at this stage and being sequenced are covered, sample size is much larger than prior art in screening table Sample selected during the SNP site of mycobacterium tuberculosis pedigree is levied, therefore, it is of the present invention including SNP site 1~285 SNP set can more fully reflect overall condition of the mycobacterium tuberculosis in parting or evolution.Secondly, the present invention is above-mentioned Mycobacterium tuberculosis can be subdivided into 7 big pedigrees and 67 sub- pedigrees and M.bovis by SNP set by building chadogram Pedigree and its sub- pedigree M.bovis1, mycobacterium tuberculosis is divided into 10 or 55 sub- pedigrees than existing SNP site and Speech, further increase resolution capability, its resolution capability with optimize before 106583 SNP site set resolution capability it is basic Quite, above-mentioned SNP set of the invention both ensure that resolution ratio volume, and reducing again needs the SNP site quantity of detection, at the two it Between obtain balance.Also, parting, accuracy rate are carried out to single mycobacterium tuberculosis using above-mentioned 285 SNP sites of the present invention Height, can be sub-divided into specific Asia pedigree by single mycobacterium tuberculosis.
In some embodiments, it is above-mentioned for detecting that the reagent and/or component of SNP set include that PCR primer, molecule are visited One or more in pin, biology sensor and chip.
The invention further relates to a kind of application of mentioned reagent box in the parting or evolutionary analysis of mycobacterium tuberculosis.
The diagnosis product judged for tuberculosis infection pathogen hypotype is being prepared the invention further relates to a kind of mentioned reagent box Application in product.
The invention further relates to a kind of method that parting or evolutionary analysis are carried out to mycobacterium tuberculosis, methods described uses upper Kit is stated to detect the SNP site of mycobacterium tuberculosis.
In some embodiments, detect the SNP site method include it is following one or more：Based on gel electrophoresis SNP detection methods, DNA sequencing method, DNA chip method, denaturing high-performance liquid chromatography or mass spectroscopic assays.
In some embodiments, the SNP detection methods based on gel electrophoresis include single-strand conformation polymorphism detection method, In denaturing gradient gel electrophoresis detection method, digestion amplification polymorphism Sequence Detection method and ApoE gene detection method One or more.
In some embodiments, the mass spectroscopic assays include matrix solid-dispersion flight time mass spectrum (MALDI-TOF) detection method.
Compared with prior art, beneficial effects of the present invention are：
1), kit of the present invention, using and method in involved SNP site 1~285 be from 2372 tuberculosis branch bars Obtained in the genome sequence of bacterium and 236 key genes by genetic differentiation coefficient (Fst) and mycobacterium tuberculosis are screened The SNP site for obtaining afterwards, is to characterize each pedigree of mycobacterium tuberculosis or sub- pedigree and close with the function of mycobacterium tuberculosis Related crucial SNP site, therefore, detect that above-mentioned SNP site has to the parting and evolutionary analysis of mycobacterium tuberculosis important Meaning.
2), kit of the present invention, using and method in involved SNP site 1~285 can be by 2372 tuberculosis branches Bacillus is subdivided into 7 big pedigrees and 67 sub- pedigrees, M.bovis pedigrees and its sub- pedigree M.bovis1, and resolution ratio is significantly larger than Existing SNP site to the parting of mycobacterium tuberculosis (mycobacterium tuberculosis is divided into 55 sub- pedigrees by 62 SNP sites, or Mycobacterium tuberculosis is divided into 10 sub- pedigrees by 71 SNP sites)；The resolution capability of above-mentioned SNP site 1~285 and this hair Mycobacterium tuberculosis (is subdivided into 7 big pedigrees and 69 sub- spectrums by 106583 SNP sites not optimized in bright embodiment System, and M.bovis pedigrees and its Asia pedigree M.bovis1) substantially quite, but the required SNP site quantity used is significantly Decline, balance is obtained in resolution ratio and the SNP site quantity of required detection.
3), kit of the present invention, using and method in involved SNP site 1~285 to single mycobacterium tuberculosis When carrying out parting, its parting accuracy rate is high, and mycobacterium tuberculosis can be sub-divided into specific Asia pedigree exactly.
Brief description of the drawings
In order to illustrate more clearly of the specific embodiment of the invention or technical scheme of the prior art, below will be to specific The accompanying drawing to be used needed for implementation method or description of the prior art is briefly described, it should be apparent that, in describing below Accompanying drawing is some embodiments of the present invention, for those of ordinary skill in the art, before creative work is not paid Put, other accompanying drawings can also be obtained according to these accompanying drawings.
Fig. 1 is to gather the chadogram for building with the SNP before optimization.
Specific embodiment
Embodiment of the present invention is described in detail below in conjunction with embodiment, but those skilled in the art will Understand, the following example is merely to illustrate the present invention, and is not construed as limiting the scope of the present invention.It is unreceipted specific in embodiment Condition person, the condition advised according to normal condition or manufacturer is carried out.Agents useful for same or the unreceipted production firm person of instrument, are The conventional products that can be obtained by commercially available purchase.
Embodiment 1,
The full-length genome scope in mycobacterium tuberculosis screens SNP site according to the following steps：
1st, bacterial strain data are downloaded
The whole world 2726 plants of mycobacterium tuberculosis full-length genome data of representativeness are downloaded from ncbi database.
2nd, quality evaluation is carried out to bacterial strain sequencing data
Quality inspection assessment is carried out to bacterial strain sequencing fastq files G/C content using FastQC (version 0.10.1) softwares： (1) removal G/C content is less than 60% or more than 70% sequencing data；(2) bacterial strains of the removal SNP miss call more than 15% is surveyed Ordinal number evidence.Final 2372 plants of mycobacterium tuberculosis sequencing datas include this research.
3rd, money order receipt to be signed and returned to the sender rate is counted
Using BWA (version 0.7.12) softwares by the sequencing file money order receipt to be signed and returned to the sender of bacterial strain to mycobacterium tuberculosis reference gene In group H37rv (NC_000962.3), bacterial strain money order receipt to be signed and returned to the sender rate is counted.
4、SNP Calling
Sequence alignment will be carried out on the sequencing file money order receipt to be signed and returned to the sender of bacterial strain to tubercle bacillus reference gene group H37Rv, after comparison Sequence using samtools v 1.3 and the instruments of picard-tools v 1.112 the Sam files for generating are carried out Bam conversions, Sequence and duplicate removal treatment.Carried out according to the Bam files obtained by treatment using variation identification software Varscan v2.4.0 SNP identifies, by genome alignment quality less than 30 or base quality is cast out less than 27 SNP site.
To improve SNP site confidence level, false positive is reduced, SNP site is further filtered according to following standard： (1) minimum allelic mutation frequency is chosen to be more than in 75% and have the SNP site for supporting the site more than 20 reads；(2) Removal is distributed in mycobacterium tuberculosis PE/PPE families SNP site.
Finally, 106583 SNP sites are obtained from 2372 sequencing bacterial strains.
Embodiment 2,
The chadogram of mycobacterium tuberculosis is built according to following steps：
1st, sample filtering
Bacterial strain by G/C content less than 60% or more than 70% is given up, and bacterial strain of the money order receipt to be signed and returned to the sender rate less than 85% is given up, by SNP Bacterial strains of the miss call more than 15% is cast out.Sample set is obtained after filtering.
2nd, using SNP site constructing system chadogram：According to embodiment 1 obtain 106583 SNP sites, with M.canettii (NC_019950.1) bacterial strain is outer group's bacterial strain, and maximum likelihood is used with RAxML (version 8.2.8) software Method carries out the structure of chadogram to the bacterial strain sample after filtering, from branches of the Bootstrap value more than 95% to evolving Tree carries out pedigree point group, finally gives 7 pedigrees and includes 1 hypotype comprising 69 hypotypes and M.bovis pedigrees, 78 altogether Branch (systematic evolution tree is shown in Fig. 1).Specifically, mycobacterium tuberculosis is subdivided into following pedigree using above-mentioned SNP site：
Pedigree 1 and its sub- pedigree 1.1,1.2,1.1.1,1.1.2,1.1.2.1,1.2.1,1.2.2,1.2.3,1.2.3.1, 1.2.3.2 (totally 10 sub- pedigrees)；
Pedigree 2 and its sub- pedigree 2.1,2.2,2.2.1,2.2.2 (totally 4 sub- pedigrees)；
Pedigree 3 and its sub- pedigree 3.1,3.2 (totally 2 sub- pedigrees)；
Pedigree 4 and its sub- pedigree 4.1,4.1.1,4.1.1.1,4.1.1.2,4.1.2,4.1.2.1,4.1.2.1.1, 4.1.2.1.2,4.1.2.1.3,4.1.2.1.4,4.1.2.2,4.2,4.2.1,4.2.1.1,4.2.1.2,4.2.1.3, 4.2.2,4.2.2.1,4.3,4.3.1,4.3.1.1,4.3.2,4.3.2.1,4.4,4.4.1,4.5,4.6,4.6.1, 4.6.1.1,4.6.2,4.7,4.7.1,4.7.2,4.7.2.1,4.7.2.2,4.8,4.8.1,4.8.2,4.9,4.10, 4.10.1,4.10.1.1,4.10.1.2,4.10.2,4.10.2.1,4.10.2.2,4.11,4.11.1,4.12,4.12.1, 4.12.2,4.12.3,4.13 (totally 53 sub- pedigrees)；
Pedigree 5；
Pedigree 6；
Pedigree 7；
M.bovis pedigrees and its sub- pedigree M.bovis1.
The mycobacterium tuberculosis downloaded is annotated according to 19 RDs and spoligotyping reported in the literature With rough parting.Foregoing SNP genotyping results are compared with the result of the rough partings of LSP and spoligotyping, two are found The repeatability of person is good, and the parting effect of above-mentioned SNP site is confirmed from side.
Embodiment 3,
Optimization SNP collection merges assesses its parting effect
1st, each branch related SNP set is obtained
According to each branch, using branch in bacterial strain and remaining bacterial strain as a colony, using Genepop (version4.5.1) software calculates the genetic differentiation coefficient (Fst) of each SNP site, the SNP site from Fst more than 0.99 As pedigree associated SNP positions.
2nd, key gene same sense mutation SNP set is obtained
The same sense mutation SNP site on 236 key genes of mycobacterium tuberculosis of document report is chosen as final collection Close, branch associated SNP positions are annotated with snpEff (version 4.3c) software, then choose same on key gene Justice mutation SNP site, as final set.The synonymous SNP of the 285 pedigrees correlation for obtaining being located on key gene by screening Site.The relevant information of the related SNP site of 285 pedigrees is as follows, and the physical location of wherein SNP site is based on knot The whole genome sequence of core mycobacteria H37Rv compares what is determined, the whole genome sequence of the Mycobacterium tuberculosis H37Rv Accession Number are NC_000962.3：
3rd, parting is compared before and after SNP set optimization
Chadogram will be built by 285 SNP sites after optimization, (i.e. 106583 SNP before optimizing with SNP set Point) parting effect compare.Before optimization, mycobacterium tuberculosis 7 big pedigrees can be divided into using 106583 SNP sites With 69 sub- pedigrees, M.bovis pedigrees and sub- pedigree M.bovis1, and after optimizing, 285 SNP sites can be by tuberculosis point Branch bacillus is divided into the sub- pedigrees of 7 big pedigrees and 67, and (compared with the SNP before optimization gathers, the SNP after optimization gathers and can not segment Sub- pedigree be 2.2.2 and 3.1), M.bovis pedigrees and its sub- pedigree M.bovis1.As can be seen here, the SNP set after optimization In SNP site far less than optimization before SNP set, but its still have high parting ability, with optimization before SNP set base This is quite.
4th, SNP set parting recruitment evaluation
The complete reference genome of the mycobacterium tuberculosis of parting type known to 22 plants is downloaded from ncbi database, according to most The 285 SNP set for obtaining eventually carries out parting (referring to table 1) to these bacterial strains, and 285 SNP set are to complete reference genome Genotyping result it is consistent with bibliography.
The known reference strain gene group of table 1 is annotated
Finally it should be noted that：Various embodiments above is merely illustrative of the technical solution of the present invention, rather than its limitations；To the greatest extent Pipe has been described in detail with reference to foregoing embodiments to the present invention, but it will be understood by those within the art that：Its The technical scheme described in foregoing embodiments can still be modified, or to which part or all technical characteristic Carry out equivalent；And these modifications or replacement, the essence of appropriate technical solution is departed from various embodiments of the present invention skill The scope of art scheme.

Claims (10)

1. it is a kind of detect mycobacterium tuberculosis SNP site kit, it is characterised in that the kit include be used for detect The reagent and/or component of SNP set, the SNP set include following one or more SNP sites, the physics of the SNP site Position be based on Mycobacterium tuberculosis H37Rv whole genome sequence compare determine, the Mycobacterium tuberculosis H37Rv it is complete The Accesion Number of genome sequence are NC_000962.3：
SNP site 1：The 107791st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 2：The 108136th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 3：The 108181st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 4：The 109040th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 5：The 110395th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 6：The 111848th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 7：The 112333rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 8：The 112490th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 9：The 112734th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 10：The 113139th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 11：The 114695th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 12：The 116225th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 13：The 154049th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 14：The 200152nd on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 15：The 200377th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 16：The 200695th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 17：The 201894th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 18：The 204424th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 19：The 204502nd on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 20：The 207077th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 21：The 207590th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 22：The 208297th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 23：The 258921st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 24：The 259689th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 25：The 301341st on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 26：The 392506th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 27：The 451896th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 28：The 452064th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 29：The 500533rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 30：The 501001st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 31：The 516658th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 32：The 580011st on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 33：The 643386th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 34：The 643751st on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 35：The 644442nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 36：The 644475th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 37：The 646051st on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 38：The 646166th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 39：The 646246th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 40：The 732555th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 41：The 738045th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 42：The 752017th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 43：The 752049th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 44：The 770391st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 45：The 962104th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 46：The 962136th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 47：The 1061309th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 48：The 1129169th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 49：The 1143318th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 50：The 1149132nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 51：The 1149551st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 52：The 1150494th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 53：The 1219669th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 54：The 1219828th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 55：The 1225203rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 56：The 1228121st on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 57：The 1235550th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 58：The 1271192nd on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 59：The 1310360th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 60：The 1324571st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 61：The 1324730th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 62：The 1324997th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 63：The 1325171st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 64：The 1326802nd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 65：The 1347179th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 66：The 1377574th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 67：The 1378731st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 68：The 1386928th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 69：The 1386970th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 70：The 1421046th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 71：The 1421115th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 72：The 1421314th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 73：The 1460672nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 74：The 1486653rd on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 75：The 1494800th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 76：The 1495332nd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 77：The 1501474th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 78：The 1502126th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 79：The 1502348th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 80：The 1505476th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 81：The 1505812nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 82：The 1510163rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 83：The 1581733rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 84：The 1586540th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 85：The 1587020th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 86：The 1588462nd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 87：The 1597411st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 88：The 1656977th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 89：The 1658036th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 90：The 1706040th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 91：The 1719328th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 92：The 1719685th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 93：The 1719829th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 94：The 1776441st on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 95：The 1790486th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 96：The 1791511st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 97：The 1793509th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 98：The 1849198th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 99：The 1850089th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 100：The 1851055th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 101：The 1867845th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 102：The 1919743rd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 103：The 1919952nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 104：The 2066477th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 105：The 2066478th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 106：The 2067686th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 107：The 2095241st on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 108：The 2095536th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 109：The 2183228th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 110：The 2192357th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 111：The 2192591st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 112：The 2202589th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 113：The 2202946th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 114：The 2283874th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 115：The 2294813rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 116：The 2295025th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 117：The 2295037th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 118：The 2295046th on mycobacterium tuberculosis chromosome, its nucleotides is T/A；
SNP site 119：The 2295050th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 120：The 2296751st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 121：The 2298201st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 122：The 2300672nd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 123：The 2300950th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 124：The 2303765th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 125：The 2304076th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 126：The 2329272nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 127：The 2329474th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 128：The 2371795th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 129：The 2371796th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 130：The 2462421st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 131：The 2496838th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 132：The 2505093rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 133：The 2512762nd on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 134：The 2514875th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 135：The 2527686th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 136：The 2547004th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 137：The 2547251st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 138：The 2549266th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 139：The 2549313rd on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 140：The 2549735th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 141：The 2610132nd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 142：The 2610354th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 143：The 2654653rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 144：The 2654706th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 145：The 2672399th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 146：The 2672617th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 147：The 2672916th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 148：The 2673609th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 149：The 2673711st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 150：The 2673858th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 151：The 2681585th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 152：The 2682603rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 153：The 2775550th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 154：The 2789351st on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 155：The 2789808th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 156：The 2789851st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 157：The 2790588th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 158：The 2810392nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 159：The 2810826th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 160：The 2817168th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 161：The 2818256th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 162：The 2859840th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 163：The 2860223rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 164：The 2860313rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 165：The 2872966th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 166：The 2884007th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 167：The 2996922nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 168：The 2997335th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 169：The 3012844th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 170：The 3016914th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 171：The 3016953rd on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 172：The 3017144th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 173：The 3017286th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 174：The 3050372nd on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 175：The 3051081st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 176：The 3118829th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 177：The 3118986th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 178：The 3151823rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 179：The 3152267th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 180：The 3152431st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 181：The 3169022nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 182：The 3194244th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 183：The 3219800th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 184：The 3285955th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 185：The 3286799th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 186：The 3332286th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 187：The 3332665th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 188：The 3336871st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 189：The 3401962nd on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 190：The 3402521st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 191：The 3423423rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 192：The 3423655th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 193：The 3424459th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 194：The 3424865th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 195：The 3453393rd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 196：The 3471148th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 197：The 3536291st on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 198：The 3536836th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 199：The 3537013rd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 200：The 3606624th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 201：The 3612568th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 202：The 3626906th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 203：The 3651143rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 204：The 3664476th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 205：The 3722442nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 206：The 3786035th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 207：The 3786186th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 208：The 3817476th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 209：The 3817994th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 210：The 3913600th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 211：The 3921273rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 212：The 3959715th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 213：The 3973331st on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 214：The 3979502nd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 215：The 3980169th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 216：The 3980398th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 217：The 3981350th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 218：The 3981601st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 219：The 3984549th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 220：The 3985105th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 221：The 3996273rd on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 222：The 3996826th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 223：The 4016684th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 224：The 4030438th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 225：The 4054217th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 226：The 4054902nd on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 227：The 4056097th on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 228：The 4056172nd on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 229：The 4070666th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 230：The 4090261st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 231：The 4090846th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 232：The 4092848th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 233：The 4095906th on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 234：The 4125161st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 235：The 4139309th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 236：The 4168881st on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 237：The 4168949th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 238：The 4201713rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 239：The 4243424th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 240：The 4243509th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 241：The 4243638th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 242：The 4244433rd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 243：The 4244598th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 244：The 4244813rd on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 245：The 4245203rd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 246：The 4245233rd on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 247：The 4245325th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 248：The 4246500th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 249：The 4267450th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 250：The 4267825th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 251：The 4268036th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 252：The 4268751st on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 253：The 4273752nd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 254：The 4274020th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 255：The 4327554th on mycobacterium tuberculosis chromosome, its nucleotides is G/C；
SNP site 256：The 4340528th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 257：The 4340731st on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 258：The 4343857th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 259：The 4344236th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 260：The 4345214th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 261：The 4345215th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 262：The 4345598th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 263：The 4347515th on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 264：The 4347938th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 265：The 4348596th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 266：The 4349307th on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 267：The 4354191st on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 268：The 4355319th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 269：The 4355324th on mycobacterium tuberculosis chromosome, its nucleotides is A/C；
SNP site 270：The 4355393rd on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 271：The 4355616th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 272：The 4362057th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 273：The 4362473rd on mycobacterium tuberculosis chromosome, its nucleotides is A/G；
SNP site 274：The 4362562nd on mycobacterium tuberculosis chromosome, its nucleotides is C/G；
SNP site 275：The 4362656th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 276：The 4362746th on mycobacterium tuberculosis chromosome, its nucleotides is T/G；
SNP site 277：The 4363247th on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 278：The 4363345th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 279：The 4396673rd on mycobacterium tuberculosis chromosome, its nucleotides is C/A；
SNP site 280：The 4397307th on mycobacterium tuberculosis chromosome, its nucleotides is G/T；
SNP site 281：The 4398213rd on mycobacterium tuberculosis chromosome, its nucleotides is T/C；
SNP site 282：The 4398910th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 283：The 4399563rd on mycobacterium tuberculosis chromosome, its nucleotides is C/T；
SNP site 284：The 4399600th on mycobacterium tuberculosis chromosome, its nucleotides is G/A；
SNP site 285：The 4400036th on mycobacterium tuberculosis chromosome, its nucleotides is G/C.
2. kit as claimed in claim 1, it is characterised in that the SNP set includes 50~285 SNP sites, Or 100~285 SNP sites, or 200~285 SNP sites, or 250~285 SNP sites.
3. kit as claimed in claim 2, it is characterised in that the SNP set includes 285 above-mentioned SNP sites.
4. kit as claimed in claim 1, it is characterised in that the reagent and/or component bag for detecting SNP set Include one or more in PCR primer, molecular probe, biology sensor and chip.
5. application of the kit described in any one of Claims 1 to 4 in the parting or evolutionary analysis of mycobacterium tuberculosis.
6. kit described in any one of Claims 1 to 4 is preparing the diagnosis product for the judgement of tuberculosis infection pathogen hypotype Application in product.
7. a kind of method that parting or evolutionary analysis are carried out to mycobacterium tuberculosis, it is characterised in that methods described usage right It is required that kit is detected to the SNP site of mycobacterium tuberculosis described in 1~4 any one.
8. method as claimed in claim 7, it is characterised in that the method for the detection SNP site includes following a kind of or several Kind：
SNP detection methods, DNA sequencing method, DNA chip method, denaturing high-performance liquid chromatography or Mass Spectrometer Method based on gel electrophoresis Method.
9. method as claimed in claim 8, it is characterised in that the SNP detection methods based on gel electrophoresis include single-stranded structure As polymorphic detection method, denaturing gradient gel electrophoresis detection method, digestion amplification polymorphism Sequence Detection method and allele specific One or more in property PCR detection methods.
10. method as claimed in claim 8, it is characterised in that the mass spectroscopic assays include matrix assisted laser desorption ionization Ionization time of flight mass spectrometry detection method.
CN201710063939.6A 2017-02-04 2017-02-04 Kit used for mycobacterium tuberculosis typing SNP site and application thereof Pending CN106701979A (en)

Priority Applications (1)

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110453001A (en) * 2019-08-28 2019-11-15 北京市结核病胸部肿瘤研究所 Application of 1073 SNP sites in mycobacterium tuberculosis pedigree 3
CN116254356A (en) * 2023-03-31 2023-06-13 首都医科大学附属北京胸科医院 Method for identifying mycobacterium tuberculosis pedigree 2.3 subtype strain and application thereof

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
FRANCESC COLL等: ""A robust SNP barcode for typing Mycobacterium tuberculosis complex strains"", 《NATURE COMMUNICATIONS》 *
INGRID FILLIOL等: ""Global Phylogeny of Mycobacterium tuberculosis Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set"", 《JOURNAL OF BACTERIOLOGY》 *
张志等: ""结核分枝杆菌基因分型技术研究进展"", 《河北北方学院学报（自然科学版）》 *

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110453001A (en) * 2019-08-28 2019-11-15 北京市结核病胸部肿瘤研究所 Application of 1073 SNP sites in mycobacterium tuberculosis pedigree 3
CN110453001B (en) * 2019-08-28 2022-11-11 北京市结核病胸部肿瘤研究所 Application of 1073 SNP sites in mycobacterium tuberculosis pedigree 3
CN116254356A (en) * 2023-03-31 2023-06-13 首都医科大学附属北京胸科医院 Method for identifying mycobacterium tuberculosis pedigree 2.3 subtype strain and application thereof
CN116254356B (en) * 2023-03-31 2024-04-30 首都医科大学附属北京胸科医院 Method for identifying mycobacterium tuberculosis pedigree 2.3 subtype strain and application thereof

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