CN104131094A - Primer composition for lysosomal disease gene screening and kit using the same - Google Patents
Primer composition for lysosomal disease gene screening and kit using the same Download PDFInfo
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Abstract
The invention provides a primer composition for lysosomal disease gene screening and a kit using the same. The primer composition comprises multiple primer sequences respectively aiming at non-repetitive regions of IDUA, ARSB, MAN2B1, ST3GAL5, SMPD1, CTNS, MFSD8, IDS, GUSB, GBA, ARSA, GNPTAB, SLC17A5, CLN8, SGSH, HYAL1, PSAP, GNPTAG, PPT1, CTSD, NAGLU, FUCA1, GLB1, SUMF1, MCOLN1, TPP1, HGSNAT, NAGA, GM2A, GALC, LIPA, CLN3, GALNS, NEU1, HEXA, GLA, NPC1, CLN5, MANBA, HEXB, ASAH1, NPC2 and CLN6 genes.
Description
Technical field
The present invention relates to detection kit field, specifically, relate to a kind of primer sets compound and test kit for lysosomal disease gene screening.
Background technology
Lysosomal disease is because genetic flaw makes to lack certain lytic enzyme in lysosome, causes corresponding effect substrate can not be degraded and put aside in lysosome, causes cellular metabolism obstacle and causes disease.Lysosomal disease is the disease that a class comprises nearly 50 kinds of enzyme defects.The sickness rate of single lysosomal disease is lower, but is about 1:6000-7000 as its sickness rate in crowd of a class disease.In Chinese annual 1600 ten thousand newborn infants, nearly 2700 people suffer from lysosomal disease according to statistics.Lysosomal disease in infant and adolescence onset, is specified pathogenesis and Disease-causing gene mostly, and early diagnosis and antenatal diagnosis have vital meaning for successive treatment and quality of life of patients.
At present, diagnosis lysosomal disease adopts the method for enzyme activity assay more, examination point mutation usually adopts the method combining with range gene sudden change detection technique taking PCR as basic polyacrylamide gel electrophoresis, mostly is a technical scheme and diagnoses a kind of disease, and flux is lower.Because lysosomal disease relates to various diseases, and these disease clinical manifestations are mostly identical, defficulty in diagnosing, and these methods often have some limitations in the time meeting the needs of clinical detection transgenation.Therefore, find effective, quick, economic, simple lysosomal disease diagnostic techniques, reduce children/mankind mortality ratio and disability rate, become a difficult problem urgently to be resolved hurrily in guarantee children's health.
Summary of the invention
In order to solve problems of the prior art, the object of this invention is to provide a kind of primer sets compound and test kit for lysosomal disease gene screening.
In order to realize the object of the invention, first the present invention provides a kind of primer sets compound for lysosomal disease gene screening, and described primer sets compound comprises respectively for IDUA (ID:3425), ARSB (ID:411), MAN2B1 (ID:4125), ST3GAL5 (ID:8869), SMPD1 (ID:6609), CTNS (ID:1497), MFSD8 (ID:256471), IDS (ID:3423), GUSB (ID:2990), GBA (ID:2629), ARSA (ID:410), GNPTAB (ID:79158), SLC17A5 (ID:26503), CLN8 (ID:2055), SGSH (ID:6448), HYAL1 (ID:3373), PSAP (ID:5660), GNPTAG (ID:2795), PPT1 (ID:5538), CTSD (ID:1509), NAGLU (ID:4669), FUCA1 (ID:2517), GLB1 (ID:2720), SUMF1 (ID:285362), MCOLN1 (ID:57192), TPP1 (ID:1200), HGSNAT (ID:138050), NAGA (ID:4668), GM2A (ID:2760), GALC (ID:2581), LIPA (ID:3988), CLN3 (ID:1201), GALNS (ID:2588), NEU1 (ID:4758), HEXA (ID:3073), GLA (ID:2717), NPC1 (ID:4864), CLN5 (ID:1203), , MANBA (ID:4126), HEXB (ID:3074), ASAH1 (ID:427), multiple primer sequences of NPC2 (ID:10577) and the non-repeat region of CLN6 (ID:54982) gene.
Further, described primer sets compound specifically comprises following primer sequence:
1) for the primer sequence of IDUA gene
2) for the primer sequence of ARSB gene
3) for the primer sequence of MAN2B1 gene
4) for the primer sequence of ST3GAL5 gene
5) for the primer sequence of SMPD1 gene
6) for the primer sequence of CTNS gene
7) for the primer sequence of MFSD8 gene
8) for the primer sequence of IDS gene
9) for the primer sequence of GUSB gene
10) for the primer sequence of GBA gene
11) for the primer sequence of ARSA gene
12) for the primer sequence of GNPTAB gene
13) for the primer sequence of SLC17A5 gene
14) for the primer sequence of CLN8 gene
15) for the primer sequence of SGSH gene
16) for the primer sequence of HYAL1 gene
17) for the primer sequence of PSAP gene
18) for the primer sequence of GNPTAG gene
19) for the primer sequence of PPT1 gene
20) for the primer sequence of CTSD gene
21) for the primer sequence of NAGLU gene
22) for the primer sequence of FUCA1 gene
23) for the primer sequence of GLB1 gene
24) for the primer sequence of SUMF1 gene
25) for the primer sequence of MCOLN1 gene
26) for the primer sequence of TPP1 gene
27) for the primer sequence of HGSNAT gene
28) for the primer sequence of NAGA gene
29) for the primer sequence of GM2A gene
30) for the primer sequence of GALC gene
31) for the primer sequence of LIPA gene
32) for the primer sequence of CLN3 gene
33) for the primer sequence of GALNS gene
34) for the primer sequence of NEU1 gene
35) for the primer sequence of HEXA gene
36) for the primer sequence of GLA gene
37) for the primer sequence of NPC1 gene
38) for the primer sequence of CLN5 gene
39) for the primer sequence of MANBA gene
40) for the primer sequence of HEXB gene
41) for the primer sequence of ASAH1 gene
42) for the primer sequence of NPC2 gene
43) for the primer sequence of CLN6 gene
The present invention also provides the test kit for lysosomal disease gene screening, and described test kit comprises aforementioned primer sets compound.
Further, described test kit also comprises: 5x PCR ion amplification mix (0.1U TagPolymerase/ μ l, 500 μ M dNTP, 20mM Tris-HCl (PH8.3), 100mM KCl, 3mM MgCl
2), 96 orifice plates, 96 orifice plate sealed membranes.
Beneficial effect of the present invention is:
Primer sets compound of the present invention and test kit can be once stored up disease (5 types), sphingolipid metabolism obstacle (15 types), glutinous fat disease (4 types), lipid to mucopolysaccharidosis (10 types), oligosaccharides and are stored up 49 kinds of lysosomal diseases such as disease (3 types), lysosome transit barrier (3 types) and neurone ceroid lipofuscin storage disorders (9 types) and carry out gene diagnosis (disease of specifically diagnosing is in table 1), molecular diagnosis fraction of coverage to lysosomal disease reaches more than 90%, specificity is good, highly sensitive.Well change and once tested the present situation that can only detect one type of disease in the past, greatly improved detection efficiency, can specify pathogenesis and Disease-causing gene, also had important meaning for follow-up treatment.
49 kinds of lysosomal diseases of table 1 and corresponding gene
Embodiment
Following examples are used for illustrating the present invention, but are not used for limiting the scope of the invention.
Embodiment 1 is for the primer sets compound of lysosomal disease gene screening
According to disclosed IDUA (ID:3425) in Genbank, ARSB (ID:411), MAN2B1 (ID:4125), ST3GAL5 (ID:8869), SMPD1 (ID:6609), CTNS (ID:1497), MFSD8 (ID:256471), IDS (ID:3423), GUSB (ID:2990), GBA (ID:2629), ARSA (ID:410), GNPTAB (ID:79158), SLC17A5 (ID:26503), CLN8 (ID:2055), SGSH (ID:6448), HYAL1 (ID:3373), PSAP (ID:5660), GNPTAG (ID:2795), PPT1 (ID:5538), CTSD (ID:1509), NAGLU (ID:4669), FUCA1 (ID:2517), GLB1 (ID:2720), SUMF1 (ID:285362), MCOLN1 (ID:57192), TPP1 (ID:1200), HGSNAT (ID:138050), NAGA (ID:4668), GM2A (ID:2760), GALC (ID:2581), LIPA (ID:3988), CLN3 (ID:1201), GALNS (ID:2588), NEU1 (ID:4758), HEXA (ID:3073), GLA (ID:2717), NPC1 (ID:4864), CLN5 (ID:1203), , MANBA (ID:4126), HEXB (ID:3074), ASAH1 (ID:427), NPC2 (ID:10577) and CLN6 (ID:54982) gene order, for the primer sequence of the exon of said gene Sequence annotation and the zone design 18-40bp length of exon and intron boundary, the amplified production length obtaining is between 125-175bp.Obtain sequence composition described in specification sheets.
Embodiment 2 is for the test kit of lysosomal disease gene screening
Described in the present embodiment, test kit mainly comprises: 2x primer sets compound, 5x PCR ion amplification mix (PCR damping fluid, dNTPs, Taq enzyme etc.), 96 orifice plates and 96 orifice plate sealed membranes.
Following composition (being provided by Life technologies company) is also provided described test kit:
Ion?Xpress?Barcode?Adaptors?1-16?Kit(Cat.no.4471250)；
MyOne
TM?Streptavidin?C1?beads(Cat.no.IVGN65001)；
Ion?PI
TM?Template?OT2?200?Kit?v3(Cat.no.4488318)；
Ion?Library?Quantitation?Kit(Cat.no.4468802)。
Embodiment 3 is for the application of the test kit of lysosomal disease gene screening
1. sample requirement
More than requiring DNA sample 30ng.
The structure in 2.DNA library
The target area of 2.1 pcr amplification genomic dnas
2.1.1 each DNA and primer sets compound are mixed, and 5XPCR ion amplification mix (PCR damping fluid, dNTPs, Taq enzyme etc.) and deionized water add in each reacting hole of PCR96 orifice plate.As the 20ul system that increases, 5X PCR ion amplification mix adds 4ul, and primer sets compound adds 10ul, and deionized water adds 5ul, and DNA sample adds 10ng.
2.1.2 with 96 orifice plate sealed membrane sealing PCR plates, fully shake, simple centrifugal PCR plate reclaims sample as far as possible to pipe bottom.Then be placed in PCR instrument, the program of moving is with target area in amplification gene group.
2.2 digestion part primer sequences
2.2.1 solution after reaction is collected the pipe end by mild centrifugation PCR plate.Slowly take the sealer of 96 orifice plates off.In each mixed reaction solution, add 2 microlitre FuPa Reagent (Life technologies), total system reaches 22 microlitres.
2.2.2 use 96 orifice plate sealed membranes that 96 orifice plates are tamping, fully vibration mixes, mild centrifugation by liquid collecting to managing at the end (also can select with rifle draw liquid over half blow and beat up and down mix at least 5 times).
2.2.3 96 hole versions are put into PCR instrument, by following program operation.
Joint is connected to amplified production purifying by 2.3
If 2.3.1 have visible throw out in Switch (Life technologies) solution, dissolve also resuspended by concussion under room temperature or upper and lower pressure-vaccum.
2.3.2 carefully remove the sealer on PCR plate and add following composition to digest sample in each reacting hole.Before adding, can first mix Switch solution and joint.
2.3.3 in each reacting hole, add 2 microlitre DNA ligases.
2.3.4 use 96 orifice plate sealed membranes that 96 orifice plates are tamping, fully vibration mixes, mild centrifugation by liquid collecting to managing at the end (also can select with rifle draw liquid over half blow and beat up and down mix at least 5 times).
2.3.5 96 hole versions are put into PCR instrument, by following program operation.
The library that 2.4 purifying do not increase
Use
xP reagent 1.5x sample volume.
2.4.1 throw off carefully shrouding film and to adding 45 microlitres (1.5x sample volume) in each library
xP reagent.Blow and beat and make for 5 times DNA and bead suspension fully mix with rifle.
2.4.2 mixed solution is placed in to room temperature 5 minutes.
2.4.3 96 orifice plates are placed on magnetic frame, leave standstill 2 minutes or wait solution change limpid.Siphon away carefully and discard supernatant, not disturbance magnetic bead.
2.4.4 in hole, add freshly prepared 70% ethanol of 150 μ L, 96 orifice plates that move around on magnetic force wash magnetic bead, then supernatant discarded carefully, not disturbance magnetic bead.
2.4.5 repeat the 4th step, wash for the second time.
2.4.6 guarantee that ethanol drop all siphons away from hole.Plate is positioned on magnetic frame, and dry 5 minutes of air at room temperature, notes not over-drying.
2.4.7 96 orifice plates are taken away from magnetic frame, in every hole, added 50 μ L Low TE fully to infiltrate magnetic bead.Use 96 orifice plate sealed membranes that 96 orifice plates are tamping, fully vibration mixes, mild centrifugation by liquid collecting to managing at the end (also can select with rifle draw liquid over half blow and beat up and down mix at least 5 times).
2.4.8 96 orifice plates are placed in to magnetic frame upper 2 minute.In supernatant liquor, contain library.Take out 5 μ L supernatants, in conjunction with the seedless sour water of 495 μ L, quantitative for library.
2.5 libraries quantitatively and dilution
Determine the concentration of Ion Ampliseq library by qPCR test kit Ion Library Quantitation Kit (Cat.no.4468802).Each sample, standard library and negative control must do twice technology and repeat in 20 microlitre reaction systems.
The common output in exon library is at 100-500pM.
The E.coli DH10B standard library (original concentration 68Pm, this library is as for Ion Library Quantitation Kit) of 2.5.1 preparing 3 continuous 10 times of dilutions respectively concentration is 6.8pM, 0.68pM, 0.068pM.These record these concentration mark as standard library with in quantitative PCR instrument software.
2.5.2 ready reaction mixing solutions.To each sample, contrast and standard library, all mix 20 microlitre 2X
the 20X Ion of MasterMix and 2 microlitres
assay also mixes.The mixed solution of packing 11 microlitres is in each PCR reacting hole.
2.5.3 add the Ion AmpliSeq library of 100 times of dilutions of 9 microlitres or each standard library of having diluted of 9 microlitres to (repetition is done in two PCR holes of each sample) in each PCR reacting hole.Total reaction system 20 microlitres.
2.5.4 the response procedures of editing quantitative PCR instrument is as follows:
The concentration in the standard library that input has been diluted;
ROX
tMwith reference to fluorescence as a setting with reference to fluorescence;
Selective reaction system 20 microlitres;
TaqMan probes report and cancellation: FAM dye/MGB
Ion Library TaqMan qPCR Mix can be used on multiple quantitative PCR instrument.The cycling program of following table can be used as the general rules of this test kit of application.Rapid Circulation pattern is StepOnePlus
tMthe recommendation pattern of system.
2.5.5, after qPCR reaction finishes, calculate the mean concns of Ion AmpliSeq library of undiluted mistake by the quantitative result of qPCR being multiplied by 100 extension rate.
2.5.6 the library concentration based on above calculating, confirms that library is diluted to 100pM by extension rate.
For example:
300pM when undiluted library concentration, the dilution factor of that library should be 300pM/100pM=3.
Therefore the Low TE (1 to 3 dilution) that, 2 microlitres are mixed in the library of 1 microlitre obtains 100pM.
2.5.7 dilute library after 100pM, next carry out the mixing of multiple libraries or template preparation.
2.6 store library
Library can be stored in 48 DEG C maximum one month, also can under 20 DEG C of conditions, store the longer time.
The order-checking of two generations is carried out in the library building.
Although above the present invention is described in detail with a general description of the specific embodiments, on basis of the present invention, can make some modifications or improvements it, this will be apparent to those skilled in the art.Therefore, these modifications or improvements without departing from theon the basis of the spirit of the present invention, all belong to the scope of protection of present invention.
Claims (4)
1. for the primer sets compound of lysosomal disease gene screening, it is characterized in that, described primer sets compound comprises respectively for IDUA, ARSB, MAN2B1, ST3GAL5, SMPD1, CTNS, MFSD8, IDS, GUSB, GBA, ARSA, GNPTAB, SLC17A5, CLN8, SGSH, HYAL1, PSAP, GNPTAG, PPT1, CTSD, NAGLU, FUCA1, GLB1, SUMF1, MCOLN1, TPP1, HGSNAT, NAGA, GM2A, GALC, LIPA, CLN3, GALNS, NEU1, HEXA, GLA, NPC1, CLN5, MANBA, HEXB, ASAH1, multiple primer sequences of the non-repeat region of NPC2 and CLN6 gene.
2. primer sets compound according to claim 1, is characterized in that, described primer sets compound specifically comprises following primer sequence:
1) for the primer sequence of IDUA gene
2) for the primer sequence of ARSB gene
3) for the primer sequence of MAN2B1 gene
4) for the primer sequence of ST3GAL5 gene
5) for the primer sequence of SMPD1 gene
6) for the primer sequence of CTNS gene
7) for the primer sequence of MFSD8 gene
8) for the primer sequence of IDS gene
9) for the primer sequence of GUSB gene
10) for the primer sequence of GBA gene
11) for the primer sequence of ARSA gene
12) for the primer sequence of GNPTAB gene
13) for the primer sequence of SLC17A5 gene
14) for the primer sequence of CLN8 gene
15) for the primer sequence of SGSH gene
16) for the primer sequence of HYAL1 gene
17) for the primer sequence of PSAP gene
18) for the primer sequence of GNPTAG gene
19) for the primer sequence of PPT1 gene
20) for the primer sequence of CTSD gene
21) for the primer sequence of NAGLU gene
22) for the primer sequence of FUCA1 gene
23) for the primer sequence of GLB1 gene
24) for the primer sequence of SUMF1 gene
25) for the primer sequence of MCOLN1 gene
26) for the primer sequence of TPP1 gene
27) for the primer sequence of HGSNAT gene
28) for the primer sequence of NAGA gene
29) for the primer sequence of GM2A gene
30) for the primer sequence of GALC gene
31) for the primer sequence of LIPA gene
32) for the primer sequence of CLN3 gene
33) for the primer sequence of GALNS gene
34) for the primer sequence of NEU1 gene
35) for the primer sequence of HEXA gene
36) for the primer sequence of GLA gene
37) for the primer sequence of NPC1 gene
38) for the primer sequence of CLN5 gene
39) for the primer sequence of MANBA gene
40) for the primer sequence of HEXB gene
41) for the primer sequence of ASAH1 gene
42) for the primer sequence of NPC2 gene
43) for the primer sequence of CLN6 gene
3. for the test kit of lysosomal disease gene screening, it is characterized in that, described test kit comprises the primer sets compound described in claim 1 or 2.
4. test kit according to claim 3, is characterized in that, described test kit comprises: the amplification of 5x PCR ion mix, 96 orifice plates and 96 orifice plate sealed membranes.
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Cited By (6)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN105385779A (en) * | 2015-12-29 | 2016-03-09 | 北京泱深生物信息技术有限公司 | Genetic marker associated with rectal adenocarcinoma |
| CN107058531A (en) * | 2017-04-01 | 2017-08-18 | 杭州艾迪康医学检验中心有限公司 | A kind of kit and method for detecting Niemann-Pick disease SMPD1 gene mutations |
| CN107922932A (en) * | 2015-08-06 | 2018-04-17 | 中央研究院 | Transformation enzyme for enzyme replacement therapy |
| CN110527716A (en) * | 2019-08-14 | 2019-12-03 | 康妍葆(北京)干细胞科技有限公司 | A kind of identification method, primer sets and the kit of odontotheca stem cell |
| JP2021523227A (en) * | 2018-05-04 | 2021-09-02 | ストーク セラピューティクス，インク． | Methods and Compositions for the Treatment of Cholesteryl Ester Accumulation |
| JP2022510341A (en) * | 2018-12-05 | 2022-01-26 | ワシントン・ユニバーシティ | How to detect, prevent, recover and treat neurological disorders |
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Cited By (9)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN107922932A (en) * | 2015-08-06 | 2018-04-17 | 中央研究院 | Transformation enzyme for enzyme replacement therapy |
| CN105385779A (en) * | 2015-12-29 | 2016-03-09 | 北京泱深生物信息技术有限公司 | Genetic marker associated with rectal adenocarcinoma |
| CN105385779B (en) * | 2015-12-29 | 2019-03-01 | 成都望路医药技术有限公司 | Gene marker relevant to rectal adenocarcinoma |
| CN107058531A (en) * | 2017-04-01 | 2017-08-18 | 杭州艾迪康医学检验中心有限公司 | A kind of kit and method for detecting Niemann-Pick disease SMPD1 gene mutations |
| JP2021523227A (en) * | 2018-05-04 | 2021-09-02 | ストーク セラピューティクス，インク． | Methods and Compositions for the Treatment of Cholesteryl Ester Accumulation |
| JP2022510341A (en) * | 2018-12-05 | 2022-01-26 | ワシントン・ユニバーシティ | How to detect, prevent, recover and treat neurological disorders |
| EP3891500A4 (en) * | 2018-12-05 | 2022-08-31 | Washington University | Methods of detecting, preventing, reversing, and treating neurological diseases |
| CN110527716A (en) * | 2019-08-14 | 2019-12-03 | 康妍葆(北京)干细胞科技有限公司 | A kind of identification method, primer sets and the kit of odontotheca stem cell |
| CN110527716B (en) * | 2019-08-14 | 2022-10-04 | 康妍葆(北京)干细胞科技有限公司 | Identification method of tooth sac stem cells, primer group and kit |
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