CN116606921A - Method for detecting chromosome aneuploidy before embryo implantation - Google Patents

Method for detecting chromosome aneuploidy before embryo implantation Download PDF

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CN116606921A
CN116606921A CN202211103951.2A CN202211103951A CN116606921A CN 116606921 A CN116606921 A CN 116606921A CN 202211103951 A CN202211103951 A CN 202211103951A CN 116606921 A CN116606921 A CN 116606921A
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胡晶晶
李彩娜
崔茜
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Shanghai Pinfeng Medical Technology Co ltd
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Abstract

The invention discloses a method for detecting chromosome aneuploidy before embryo implantation, which uses a part of degenerate oligonucleotide primer to carry out PCR reaction (the primer contains 6 random bases), firstly uses lower temperature (-25 ℃) to anneal, then slowly heats up to primer extension temperature to carry out primer extension, and after the first few cycles are completed, uses higher annealing temperature (-55 ℃) to carry out multi-cycle conventional PCR reaction, thereby realizing amplification of whole genome.

Description

Method for detecting chromosome aneuploidy before embryo implantation
Technical Field
The invention relates to the technical field of assisted reproduction, in particular to a method for detecting chromosome aneuploidy before embryo implantation.
Background
The detection of chromosome aneuploidy before embryo implantation refers to a high throughput sequencing method of low depth whole genome by using embryo cells, and by performing whole genome high throughput massively parallel genome sequencing on the whole genome amplified products of single or limited embryo cells obtained and performing statistical information analysis on the whole genome sequencing results, whether the chromosome of the embryo is aneuploidy or contains a fragment of copy number variation (CNV, copy Number Variants), the chromosome of a normal embryo is a whole ploidy, namely a diploid, and the aneuploidy embryo is usually easy to cause abortion or fetal abnormality (development problem or disease), so that hospitals need to detect the chromosome aneuploidy before embryo implantation when assisted reproduction is performed on patients.
Because the detection before embryo implantation can only take a small amount of about 1-3 cells, and the whole genome DNA content of a whole set of human beings contained in each embryo cell is about 6.6pg, the whole genome amplification is needed to be carried out on very small amounts of DNA, the subsequent detection can be carried out, the method widely used for detecting the chromosome aneuploidy before embryo implantation is mainly based on MALDBAC (Multiple Annealing and Looping Based Amplification Cycles, called MALDBAC for short), namely the multi-annealing circular amplification technology is a patent technology based on the research group of Havard university Xie Xiaoliang, the technology and the unique application of the technology in the aspect of researching human sperm recombination are obvious, the operation steps are more, the human beings are easy to cause artificial deviation or error, and especially when the template copy number of DNA amplification is very low, the amplification deviation is easy to be caused, so that nonspecific amplification can occur, the final aneuploidy judgment error is influenced, meanwhile, the bioinformatics algorithm widely used for detecting the chromosome aneuploidy before embryo implantation is mainly adopts the technology which is based on the filtration technology and the technology of carrying out binary data after the filtration and the repeated cycle is carried out, and the defect that the defect of losing part of the data can be caused by the final analysis is carried out, and the defect that the data is lost after the analysis is carried out.
Disclosure of Invention
The present invention is directed to a method for detecting a chromosome aneuploidy before embryo implantation, which solves the above-mentioned problems of the prior art.
In order to achieve the above purpose, the present invention provides the following technical solutions:
a method for detecting a pre-implantation chromosomal aneuploidy of an embryo, the method comprising the steps of,
s1: whole gene amplification, including cell lysis, pre-amplification and amplification;
A. cell lysis
Reagents required at this stage: cell lysis Buffer, cell lysis enzyme, TE Buffer.
1) Preparing a cracking system: sequentially adding the following reagents into a centrifuge tube, gently swirling, mixing, briefly centrifuging, and placing into an ice box for use;
2) Preparing a sample: immediately after taking out the cell sample from the-80 ℃ refrigerator, placing the cell sample on an ice box, briefly centrifuging for about 5 seconds, immediately placing the cell sample back on the ice box, and simultaneously taking 2.5 mu L of TE Buffer as a blank control for amplification; adding TE Buffer into all samples, supplementing to 5.0 mu L, performing instantaneous centrifugation, and placing on an ice box;
3) Adding 5.0 mu L of the lysis system prepared in the first step into a sample tube respectively, and slightly and instantaneously centrifuging without shaking;
4) The PCR reaction procedure (thermal lid kept at 105 ℃) was set up and was performed as follows:
B. pre-amplification
Reagents required at this stage: pre-amplification buffer, pre-amplification enzyme; and (5) fully oscillating and uniformly mixing after melting at room temperature, and performing instantaneous centrifugation.
1) Preparing a whole genome pre-amplification reaction system according to the following table, slightly vortex mixing, briefly centrifuging, and putting into an ice box for use;
2) Taking out the sample after the cell lysis reaction from the PCR instrument, placing the sample on an ice box, adding 10.0 mu L of the whole genome pre-amplification reaction system prepared in the previous step into each sample tube, and slightly and instantaneously centrifuging without shaking;
3) The PCR reaction procedure (thermal lid kept at 105 ℃) was set up and was performed as follows:
C. amplification of
Taking out the amplification reagent and the label array (GCTCTTCCGATCTKKKKKKNNTGGG; GCTCTTCCGATCTKKKKKKNNGTTT) in advance, melting at room temperature, fully oscillating and uniformly mixing, and performing instantaneous centrifugation;
1) Preparing an amplification reaction system according to the following table, slightly vortex mixing, briefly centrifuging, and placing into an ice box for use;
2) Adding 20.0 mu L of amplification reaction system into a PCR tube of a pre-amplification product;
3) The PCR reaction procedure (thermal lid kept at 105 ℃) was set up and was performed as follows:
s2: purifying the library;
1) Mixing proper amount of 80% ethanol;
2) Before use, the purified magnetic beads are balanced to room temperature for at least 30min;
3) Adding 50 mu L of magnetic beads with equal volume into each sample, and gently vortex and mix uniformly;
4) Incubating the mixture at room temperature for 5min;
5) Centrifuging instantaneously, placing on a magnetic rack for 2min, and carefully discarding the supernatant;
6) 200 mu L of 80% ethanol prepared at present is slowly added to each sample, and the mixture is incubated for rest for 30s on a magnetic rack; the supernatant was then carefully discarded, taking care not to aspirate or disturb the beads;
7) Repeating the step 6) for two times of ethanol washing;
8) Centrifuging the residual tube wall liquid to the bottom of the tube;
9) Incubating on a magnetic rack for 2min, carefully sucking off the supernatant, opening a tube cover, and airing at room temperature until the surface of the magnetic beads is free from floodlight;
10 Resuspension the beads with 40 μl of nuclease-free water and incubating the resuspension mixture at room temperature for 2min;
11 Standing on a magnetic rack for 2min, transferring 38 mu L of supernatant to a new 1.5mLEP tube, and storing the purified library sample at-20deg.C for 1 month for on-machine sequencing, wherein the freezing and thawing times are not more than 3 times.
S3: quantifying a library;
1) Library quantification was performed on the purified library using a Qubit fluorometer: the individual library concentration should be greater than 25 ng/. Mu.L;
2) The Qsep100 biological fragment analyzer detects fragment length, and library fragments are 600-1000 bp.
S4: preparing a mixed library;
library mixing: according to the quantitative result of the Qubit, each sample is mixed by taking an equal-mass library, and if a blank control exists, the mixed quantity of the blank control is the average value of the sampling volume of the sample.
S5: adapter conversion and library denaturation;
the "MGIEasy universal library switching kit" was used, exactly according to the instructions.
S6: DNB preparation and sequencing;
the sequencing reaction was performed on a gene sequencer (MGISEQ-200) using a universal kit for sequencing reaction (combined probe-anchored sequencing by polymerization), and was performed strictly according to the instructions.
S7: analyzing data;
data analysis was performed using an embryo chromosome heteroploidy analysis system, operating strictly according to the instructions.
1) Statistics of quality control information
2) GC correction
3) Normalization
4) Cyclic binary cutting (Circular binary segmentation, CBS for short)
Autosomal CBS was analyzed using R-pack DNAcopy, where the parameter α (P-value for breakpoint detection) was set to 1e-5, each segment contained at least two bins, and finally the average of consecutive bins was used as the ratio for this segment, cyclic binary cut could improve the running speed and detection effect, and mutation information in the negative sample library was used to weight CBS and segment z-score, by which method less accurate bins could be weighted down.
5) Blacklist filtering of non-informative sites
The presence of a large number of overlapping regions in the human genome, such as microsatellites, centromeres, telomeres, can prevent the accuracy of short sequence alignments, and these sites can complicate data normalization, thus requiring the creation of a blacklist and the tag filtering of these regions to improve the accuracy of the analysis.
6) Noise cancellation and reduction
The observed median signal variance MSVo (median sigment variance), the median of a set of variances, is a measure of the noise of the sample, where each variance corresponds to the variance of one segment, and the expected median segment variance (median segment variance, MSVe for short) is inversely proportional to the memory cell size and the depth of the sequenced sequence, since both define noise, MSVo is a measure of noise. The formula is as follows:
7) Judgment result
Calculation of chromosomal abnormalities is measured using log2, expressed as the ratio of observed to expected Copy Number (CN). The formula is as follows:
chromosome deletion:
chromosome duplication:
and meanwhile, the boundary forming the distortion call at any 1/3 copy number deviation from the diploid is selected to obtain more true positive results. The specific formula is as follows:
copy number deletion:
copy number repetition:
let z score to determine if the chromosome is aneuploidy, the calculation of z score can use the following formula:
formula Z segment(n→m) The z-score, μw () representing segments of bin from n to m counts the mean value of bin using the weight value obtained by the degree of difference of bin at reference construction, m () and std ((), calculates the general mean and standard deviation, rn represents the reads ratio of the detected sample at bin, R2, n represents the reads ratio of the second sample at the same site in the reference set, and there are p healthy reference samples in total.
According to the existing negative sample library, when the Z score is smaller than-0.5, the chromosome can be judged to be a deletion result, and when the Z score is larger than 0.5, the chromosome can be judged to be a repetition result.
S8: viewing reports
a) If the z score value of a chromosome in the detection sample is more than or equal to 0.5 or less than or equal to-0.5, the chromosome of the sample is abnormal, otherwise, the detection does not find the abnormal aneuploidy.
b) If the z-score value of a chromosome is 0, it should be determined that the chromosome is not detected by the sample, and for autosomes, the detection result is positive homozygous deletion, and for sex chromosomes, the detection result should be determined together with X, Y detection result;
c) For X, Y chromosome detection results, it should be commonly determined that if the X chromosome detection result is monomer and the Y chromosome detection result is monomer, then the sample X, Y chromosome detection result should be determined that no aneuploidy abnormality is found, and it cannot be determined that the monomers are positive (aneuploidy abnormality), respectively;
as a further scheme of the invention: in the step S1, in consideration of the loss in the pipetting process, a cell lysis Buffer solution, a cell lysis enzyme and a TE Buffer reagent need to be additionally prepared for preparing a lysis system during cell lysis.
As still further aspects of the invention: the 9 th item in S2 should be carefully protected from excessive drying during handling, for example, the tube cover must be closed when the magnetic beads have cracks.
As still further aspects of the invention: the statistical quality control information in S7 includes information such as statistical sequencing number (reads), number of bases, Q20 (mass value > 20), Q30 (mass value) 30, N ratio, GC content, alignment, genome Coverage (Coverage), redundancy (redundancy), and the like.
As still further aspects of the invention: the GC correction in S7 uses bwa software to align the sequenced sequence to the reference genome (version number GRCh 38), and the effective sequence of the aligned reference genome is allocated to the genome (window) of 200kb fragment size divided in advance, and then GC correction is performed, which comprises the following steps: firstly, calculating the GC content of the genome of each window region; the window sequence content (RC) is then recalculated with the ratio of the average number of sequences for all windows of the sample to the average number of sequences for windows within the GC content level as the window GC correction weight.
As still further aspects of the invention: the step of S7 is to collect a group of healthy human samples with about 100 persons in the same experimental procedure as a negative sample library, wherein the bins from the group of samples can be used as normal diploid control, the bin reference correspondence inside the samples is determined for standardization, 200kb bin is used for detecting copy number variation with abnormal size of more than 4Mb, when preparing the negative sample library, a Y chromosome fragment is used, training data is carried out under a gaussian mixture model, male and female samples are distinguished, autosomes are used as negative references for all samples, different gender groups are used for generating sex chromosome negative references, when a new sample is detected, the gender is automatically predicted, and a correct negative reference library is selected, so that the detection accuracy is improved.
Compared with the prior art, the invention has the beneficial effects that:
in order to solve the problems that the existing multiple annealing cyclic amplification technology is too high in operation steps, the template copy number of DNA amplification is extremely low and is easy to cause amplification deviation and the like due to too high operation steps, the invention uses a degenerate primer (Degenerate Oligonucleotide-Primed, DOP) PCR method and combines random primers which are designed independently to establish a specific very micro whole genome DNA amplification method.
Drawings
FIG. 1 is a flow chart of the present invention.
Fig. 2 is a visual representation of the final analysis results.
Detailed Description
The following description of the embodiments of the present invention will be made clearly and completely with reference to the accompanying drawings, in which it is apparent that the embodiments described are only some embodiments of the present invention, but not all embodiments. All other embodiments, which can be made by those skilled in the art based on the embodiments of the invention without making any inventive effort, are intended to be within the scope of the invention.
Referring to FIGS. 1-2, in one embodiment of the present invention, a method for detecting a chromosomal aneuploidy prior to embryo implantation comprises the steps of,
s1: whole gene amplification, including cell lysis, pre-amplification and amplification;
A. cell lysis
Reagents required at this stage: cell lysis Buffer, cell lysis enzyme, TE Buffer.
1) Preparing a cracking system: sequentially adding the following reagents (5% more are prepared in consideration of the loss in the pipetting process) into a centrifuge tube, gently vortex mixing, briefly centrifuging, and putting into an ice box for use;
2) Preparing a sample: immediately after taking out the cell sample from the-80 ℃ refrigerator, placing the cell sample on an ice box, briefly centrifuging for about 5 seconds, immediately placing the cell sample back on the ice box, and simultaneously taking 2.5 mu L of TE Buffer as a blank control for amplification; adding TE Buffer into all samples, supplementing to 5.0 mu L, performing instantaneous centrifugation, and placing on an ice box;
3) Adding 5.0 mu L of the lysis system prepared in the first step into a sample tube respectively, and slightly and instantaneously centrifuging without shaking;
4) The PCR reaction procedure (thermal lid kept at 105 ℃) was set up and was performed as follows:
B. pre-amplification
Reagents required at this stage: pre-amplification buffer, pre-amplification enzyme; and (5) fully oscillating and uniformly mixing after melting at room temperature, and performing instantaneous centrifugation.
1) Preparing a whole genome pre-amplification reaction system according to the following table, slightly vortex mixing, briefly centrifuging, and putting into an ice box for use;
2) Taking out the sample after the cell lysis reaction from the PCR instrument, placing the sample on an ice box, adding 10.0 mu L of the whole genome pre-amplification reaction system prepared in the previous step into each sample tube, and slightly and instantaneously centrifuging without shaking;
3) The PCR reaction procedure (thermal lid kept at 105 ℃) was set up and was performed as follows:
C. amplification of
Taking out the amplification reagent and the label array (GCTCTTCCGATCTKKKKKKNNTGGG; GCTCTTCCGATCTKKKKKKNNGTTT) in advance, melting at room temperature, fully oscillating and uniformly mixing, and performing instantaneous centrifugation;
1) Preparing an amplification reaction system according to the following table, slightly vortex mixing, briefly centrifuging, and placing into an ice box for use;
2) Adding 20.0 mu L of amplification reaction system into a PCR tube of a pre-amplification product;
3) The PCR reaction procedure (thermal lid kept at 105 ℃) was set up and was performed as follows:
s2: purifying the library;
1) Mixing proper amount of 80% ethanol;
2) Before use, the purified magnetic beads are balanced to room temperature for at least 30min;
3) Adding 50 mu L of magnetic beads with equal volume into each sample, and gently vortex and mix uniformly;
4) Incubating the mixture at room temperature for 5min;
5) Centrifuging instantaneously, placing on a magnetic rack for 2min, and carefully discarding the supernatant;
6) 200 mu L of 80% ethanol prepared at present is slowly added to each sample, and the mixture is incubated for rest for 30s on a magnetic rack; the supernatant was then carefully discarded, taking care not to aspirate or disturb the beads;
7) Repeating the step 6) for two times of ethanol washing;
8) Centrifuging the residual tube wall liquid to the bottom of the tube;
9) Incubating on a magnetic rack for 2min, carefully sucking off the supernatant, opening a tube cover, and airing at room temperature until the surface of the magnetic beads is free from floodlight (taking care to avoid excessive drying, and covering the tube cover if the magnetic beads have cracks);
10 Resuspension the beads with 40 μl of nuclease-free water and incubating the resuspension mixture at room temperature for 2min;
11 Standing on a magnetic rack for 2min, transferring 38 mu L of supernatant to a new 1.5mLEP tube, and storing the purified library sample at-20deg.C for 1 month for on-machine sequencing, wherein the freezing and thawing times are not more than 3 times.
S3: quantifying a library;
1) Library quantification was performed on the purified library using a Qubit fluorometer: the individual library concentration should be greater than 25 ng/. Mu.L;
2) The Qsep100 biological fragment analyzer detects fragment length, and library fragments are 600-1000 bp.
S4: preparing a mixed library;
library mixing: according to the quantitative result of the Qubit, each sample is mixed by taking an equal-mass library, and if a blank control exists, the mixed quantity of the blank control is the average value of the sampling volume of the sample.
S5: adapter conversion and library denaturation;
the "MGIEasy universal library switching kit" was used, exactly according to the instructions.
S6: DNB preparation and sequencing;
the sequencing reaction was performed on a gene sequencer (MGISEQ-200) using a universal kit for sequencing reaction (combined probe-anchored sequencing by polymerization), and was performed strictly according to the instructions.
S7: analyzing data;
data analysis was performed using an embryo chromosome heteroploidy analysis system, operating strictly according to the instructions.
1) Statistics of quality control information
Statistical sequencing number (reads), number of bases, Q20 (mass > 20), Q30 (mass) 30), N ratio, GC content, alignment, genome Coverage (Coverage), redundancy (redundancy), and the like.
2) GC correction
The sequenced sequences were aligned to the reference genome (version number GRCh 38) using bwa software, and the effective sequences of the aligned reference genome were assigned to the 200kb fragment sized genome (window) previously partitioned, and then GC corrected, detailed steps were: firstly, calculating the GC content of the genome of each window region; the window sequence content (RC) is then recalculated with the ratio of the average number of sequences for all windows of the sample to the average number of sequences for windows within the GC content level as the window GC correction weight.
3) Normalization
A set of healthy human samples of about 100 persons of the same experimental procedure were collected as a negative sample library, the bins from this set of samples could be used as normal diploid controls, the bin reference correspondence inside the samples was determined for normalization, a 200kb bin was used for detection of abnormal size variations above 4 Mb.
When preparing a negative sample library, training data under a Gaussian mixture model by using Y chromosome fragments, distinguishing male and female samples, using autosomes as negative references for all samples, generating sex chromosome negative references by different gender groups, automatically predicting gender when detecting a new sample, and selecting a correct negative reference library to improve detection accuracy.
4) Cyclic binary cutting (Circular binary segmentation, CBS for short)
Autosomal CBS was analyzed using R-pack DNAcopy, where the parameter α (P-value for breakpoint detection) was set to 1e-5, each segment contained at least two bins, and finally the average of consecutive bins was used as the ratio for this segment, cyclic binary cut could improve the running speed and detection effect, and mutation information in the negative sample library was used to weight CBS and segment z-score, by which method less accurate bins could be weighted down.
5) Blacklist filtering of non-informative sites
The presence of a large number of overlapping regions in the human genome, such as microsatellites, centromeres, telomeres, can prevent the accuracy of short sequence alignments, and these sites can complicate data normalization, thus requiring the creation of a blacklist and the tag filtering of these regions to improve the accuracy of the analysis.
6) Noise cancellation and reduction
The observed median signal variance MSVo (median sigment variance), the median of a set of variances, is a measure of the noise of the sample, where each variance corresponds to the variance of one segment, and the expected median segment variance (mediansegment variance, MSVe for short) is inversely proportional to the memory cell size and the depth of the sequenced sequence, since both define noise, MSVo is a measure of noise. The formula is as follows:
7) Judgment result
Calculation of chromosomal abnormalities is measured using log2, expressed as the ratio of observed to expected Copy Number (CN). The formula is as follows:
chromosome deletion:
chromosome duplication:
and meanwhile, the boundary forming the distortion call at any 1/3 copy number deviation from the diploid is selected to obtain more true positive results. The specific formula is as follows:
copy number deletion:
copy number repetition:
let z score to determine if the chromosome is aneuploidy, the calculation of z score can use the following formula:
formula Z segment(n→m) The z-score, μw () representing segments of bin from n to m counts the mean value of bin using the weight value obtained by the degree of difference of bin at reference construction, m () and std ((), calculates the general mean and standard deviation, rn represents the reads ratio of the detected sample at bin, R2, n represents the reads ratio of the second sample at the same site in the reference set, and there are p healthy reference samples in total.
According to the existing negative sample library, when the Z score is smaller than-0.5, the chromosome can be judged to be a deletion result, and when the Z score is larger than 0.5, the chromosome can be judged to be a repetition result.
S8: viewing reports
a) If the z score value of a chromosome in the detection sample is more than or equal to 0.5 or less than or equal to-0.5, the chromosome of the sample is abnormal, otherwise, the detection does not find the abnormal aneuploidy.
b) If the z-score value of a chromosome is 0, it should be determined that the chromosome is not detected by the sample, and for autosomes, the detection result is positive homozygous deletion, and for sex chromosomes, the detection result should be determined together with X, Y detection result;
c) For X, Y chromosome detection results, it should be collectively determined that if the X chromosome detection result is a single body and the Y chromosome detection result is a single body, then this sample X, Y chromosome detection result should be determined that no aneuploidy abnormality is found, and it cannot be determined that the single body is positive (aneuploidy abnormality), respectively.
The invention introduces a degenerate oligonucleotide primer PCR (degenerate oligonucleotide primed PCR, DOP-PCR) technology, which uses a part of degenerate oligonucleotide primer to carry out PCR reaction (the primer contains 6 random bases in the middle), firstly uses lower temperature (25 ℃) to anneal, then slowly heats up to primer extension temperature to carry out primer extension, and after the first few cycles are completed, uses higher annealing temperature (55 ℃) to carry out multi-cycle conventional PCR reaction, thereby realizing the amplification of the whole genome.
The working principle of the invention is as follows:
amplifying and banking cells obtained from embryo in blastula stage, sequencing the amplified product on whole genome level by using combined probe anchored polymerization sequencing method, analyzing the sequencing result by bioinformatic software to judge whether the embryo has abnormal chromosome aneuploidy number;
embryo cell whole genome amplification is performed in a manner with low amplification preference to maintain sample raw DNA information as unbiased as possible. The amplification is performed in three steps: lysis, pre-amplification and amplification. After the embryo cells are lysed, the genome is pre-amplified by using random primers with special structures and matched components, so that a pre-amplified product with relatively stable structures is formed. Finally, carrying out exponential amplification on the genome by using an amplification primer matched with the sequence of the non-random part of the pre-amplification primer and a matched component, and simultaneously adding a sequencing joint and a sample identification tag sequence;
performing whole genome sequencing by using a combined probe anchored polymerization sequencing method (MGISEQ-200), analyzing a sequencing result by using bioinformatics software to obtain the number of effective sequences matched to each chromosome, and calculating the ratio of the number of the effective sequences to the number of corresponding chromosome sequences in a reference database; if the ratio is too high, the chromosome may be judged as trisomy or duplication; if the ratio is too low, the chromosome can be judged to be a monomer or a deletion, so that the detection of the chromosome non-integral abnormality is realized.
The following table is the main product components
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Sample requirement
1. Sample type:
blastocyst stage trophoblast biopsy samples.
2. Sample collection:
fertilized eggs are cultured in vitro to the blastula stage, blastula stage embryos are sampled according to a conventional embryo biopsy technique, at least 3 cells are taken as samples to be examined, the biopsied embryo cells are washed 3 times with 1 XPBS buffer (without Ca2+ and Mg2+), and then the washed cells (approximately containing 0.5 μL of 1 XPBS buffer) are carefully transferred into a PCR tube containing 2.0 μL of 1 XPBS buffer in a volume of not more than 2.5 μL.
3. Sample transportation:
transporting under dry ice conditions; it is necessary to ensure that there is enough dry ice remaining when the sample is delivered and a buffer device is provided to prevent the sample tube from being crushed by the dry ice during transportation. And (3) transporting by using dry ice, wherein the transportation time is not longer than 3 days, and if the transportation time is longer than 3 days, the frozen products (dry ice) need to be thrown in again.
4. Sample preservation
The collected cell sample should be stored in a refrigerator at-80 ℃ for no more than 12 months, and the freezing and thawing times are no more than 3 times.
Although the present invention has been described with reference to the foregoing embodiments, it will be apparent to those skilled in the art that modifications may be made to the embodiments described, or equivalents may be substituted for elements thereof, and any modifications, equivalents, improvements and changes may be made without departing from the spirit and principles of the present invention.

Claims (6)

1. A method for detecting a pre-embryo implantation chromosomal aneuploidy, characterized by: the method comprises the following steps of,
s1: whole gene amplification, including cell lysis, pre-amplification and amplification;
A. cell lysis
Reagents required at this stage: cell lysis Buffer, cell lysis enzyme, TE Buffer.
1) Preparing a cracking system: sequentially adding the following reagents into a centrifuge tube, gently swirling, mixing, briefly centrifuging, and placing into an ice box for use;
2) Preparing a sample: immediately after taking out the cell sample from the-80 ℃ refrigerator, placing the cell sample on an ice box, briefly centrifuging for about 5 seconds, immediately placing the cell sample back on the ice box, and simultaneously taking 2.5 mu L of TE Buffer as a blank control for amplification; adding TE Buffer into all samples, supplementing to 5.0 mu L, performing instantaneous centrifugation, and placing on an ice box;
3) Adding 5.0 mu L of the lysis system prepared in the first step into a sample tube respectively, and slightly and instantaneously centrifuging without shaking;
4) Setting a PCR instrument reaction program (the thermal cover is kept at 105 ℃);
B. pre-amplification
Reagents required at this stage: pre-amplification buffer, pre-amplification enzyme; and (5) fully oscillating and uniformly mixing after melting at room temperature, and performing instantaneous centrifugation.
1) Preparing a whole genome pre-amplification reaction system, slightly vortex mixing, briefly centrifuging, and putting into an ice box for use;
2) Taking out the sample after the cell lysis reaction from the PCR instrument, placing the sample on an ice box, adding 10.0 mu L of the whole genome pre-amplification reaction system prepared in the previous step into each sample tube, and slightly and instantaneously centrifuging without shaking;
3) Setting a PCR instrument reaction program (the thermal cover is kept at 105 ℃);
C. amplification of
Taking out the amplification reagent and the label array (GCTCTTCCGATCTKKKKKKNNTGGG; GCTCTTCCGATCTKKKKKKNNGTTT) in advance, melting at room temperature, fully oscillating and uniformly mixing, and performing instantaneous centrifugation;
1) Preparing an amplification reaction system, slightly vortex mixing, briefly centrifuging, and putting into an ice box for use;
2) Adding 20.0 mu L of amplification reaction system into a PCR tube of a pre-amplification product;
3) Setting a PCR instrument reaction program (the thermal cover is kept at 105 ℃);
s2: purifying the library;
1) Mixing proper amount of 80% ethanol;
2) Before use, the purified magnetic beads are balanced to room temperature for at least 30min;
3) Adding 50 mu L of magnetic beads with equal volume into each sample, and gently vortex and mix uniformly;
4) Incubating the mixture at room temperature for 5min;
5) Centrifuging instantaneously, placing on a magnetic rack for 2min, and carefully discarding the supernatant;
6) 200 mu L of 80% ethanol prepared at present is slowly added to each sample, and the mixture is incubated for rest for 30s on a magnetic rack; the supernatant was then carefully discarded, taking care not to aspirate or disturb the beads;
7) Repeating the step 6) for two times of ethanol washing;
8) Centrifuging the residual tube wall liquid to the bottom of the tube;
9) Incubating on a magnetic rack for 2min, carefully sucking off the supernatant, opening a tube cover, and airing at room temperature until the surface of the magnetic beads is free from floodlight;
10 Resuspension the beads with 40 μl of nuclease-free water and incubating the resuspension mixture at room temperature for 2min;
11 Standing on a magnetic rack for 2min, transferring 38 mu L of supernatant to a new 1.5mLEP tube, and storing the purified library sample at-20deg.C for 1 month for on-machine sequencing, wherein the freezing and thawing times are not more than 3 times.
S3: quantifying a library;
1) Library quantification was performed on the purified library using a Qubit fluorometer: the individual library concentration should be greater than 25 ng/. Mu.L;
2) The Qsep100 biological fragment analyzer detects fragment length, and library fragments are 600-1000 bp.
S4: preparing a mixed library;
library mixing: according to the quantitative result of the Qubit, each sample is mixed by taking an equal-mass library, and if a blank control exists, the mixed quantity of the blank control is the average value of the sampling volume of the sample.
S5: adapter conversion and library denaturation;
the "MGIEasy universal library switching kit" was used, exactly according to the instructions.
S6: DNB preparation and sequencing;
the sequencing reaction was performed on a gene sequencer (MGISEQ-200) using a universal kit for sequencing reaction (combined probe-anchored sequencing by polymerization), and was performed strictly according to the instructions.
S7: analyzing data;
data analysis was performed using an embryo chromosome heteroploidy analysis system, operating strictly according to the instructions.
1) Statistics of quality control information
2) GC correction
3) Normalization
4) Cyclic binary cutting (Circular binary segmentation, CBS for short)
Autosomal CBS was analyzed using R-pack DNAcopy, where the parameter α (P-value for breakpoint detection) was set to 1e-5, each segment contained at least two bins, and finally the average of consecutive bins was used as the ratio for this segment, cyclic binary cut could improve the running speed and detection effect, and mutation information in the negative sample library was used to weight CBS and segment z-score, by which method less accurate bins could be weighted down.
5) Blacklist filtering of non-informative sites
The presence of a large number of overlapping regions in the human genome, such as microsatellites, centromeres, telomeres, can prevent the accuracy of short sequence alignments, and these sites can complicate data normalization, thus requiring the creation of a blacklist and the tag filtering of these regions to improve the accuracy of the analysis.
6) Noise cancellation and reduction
The observed median signal variance MSVo (median sigment variance), the median of a set of variances, is a measure of the noise of the sample, where each variance corresponds to the variance of one segment, and the expected median segment variance (median segment variance, MSVe for short) is inversely proportional to the memory cell size and the depth of the sequenced sequence, since both define noise, MSVo is a measure of noise. The formula is as follows:
7) Judgment result
Calculation of chromosomal abnormalities is measured using log2, expressed as the ratio of observed to expected Copy Number (CN). The formula is as follows:
chromosome deletion:
chromosome duplication:
and meanwhile, the boundary forming the distortion call at any 1/3 copy number deviation from the diploid is selected to obtain more true positive results. The specific formula is as follows:
copy number deletion:
copy number repetition:
let z score to determine if the chromosome is aneuploidy, the calculation of z score can use the following formula:
formula Z segment(n→m) The z-score, μw () representing segments of bin from n to M counts the mean value of bin using the weight value obtained by the degree of difference of bin at reference construction, M () and std (() calculate the general mean and standard deviation, rn represents the reads ratio of the detected sample at bin, R2, n represents the reads ratio of the second sample at the same site in the reference set, and there are p healthy reference samples in total.
According to the existing negative sample library, when the Z score is smaller than-0.5, the chromosome can be judged to be a deletion result, and when the Z score is larger than 0.5, the chromosome can be judged to be a repetition result.
S8: viewing reports
a) If the z score value of a chromosome in the detection sample is more than or equal to 0.5 or less than or equal to-0.5, the chromosome of the sample is abnormal, otherwise, the detection does not find the abnormal aneuploidy.
b) If the z-score value of a chromosome is 0, it should be determined that the chromosome is not detected by the sample, and for autosomes, the detection result is positive homozygous deletion, and for sex chromosomes, the detection result should be determined together with X, Y detection result;
c) For X, Y chromosome detection results, it should be commonly determined that if the X chromosome detection result is monomer and the Y chromosome detection result is monomer, then the sample X, Y chromosome detection result should be determined that no aneuploidy abnormality is found, and it cannot be determined that the monomers are positive (aneuploidy abnormality), respectively;
d) The final analysis results are visualized as shown.
2. A method for detecting a pre-embryo implantation chromosomal aneuploidy according to claim 1 wherein: in the step S1, in consideration of the loss in the pipetting process, a cell lysis Buffer solution, a cell lysis enzyme and a TE Buffer reagent need to be additionally prepared for preparing a lysis system during cell lysis.
3. A method for detecting a pre-embryo implantation chromosomal aneuploidy according to claim 1 wherein: the 9 th item in S2 should be carefully protected from excessive drying during handling, for example, the tube cover must be closed when the magnetic beads have cracks.
4. A method for detecting a pre-embryo implantation chromosomal aneuploidy according to claim 1 wherein: the statistical quality control information in S7 includes information such as statistical sequencing number (reads), number of bases, Q20 (mass value > 20), Q30 (mass value) 30, N ratio, GC content, alignment, genome Coverage (Coverage), redundancy (redundancy), and the like.
5. A method for detecting a pre-embryo implantation chromosomal aneuploidy according to claim 1 wherein: the GC correction in S7 uses bwa software to align the sequenced sequence to the reference genome (version number GRCh 38), and the effective sequence of the aligned reference genome is allocated to the genome (window) of 200kb fragment size divided in advance, and then GC correction is performed, which comprises the following steps: firstly, calculating the GC content of the genome of each window region; the window sequence content (RC) is then recalculated with the ratio of the average number of sequences for all windows of the sample to the average number of sequences for windows within the GC content level as the window GC correction weight.
6. A method for detecting a pre-embryo implantation chromosomal aneuploidy according to claim 1 wherein: the step of S7 is to collect a group of healthy human samples with about 100 persons in the same experimental procedure as a negative sample library, wherein the bins from the group of samples can be used as normal diploid control, the bin reference correspondence inside the samples is determined for standardization, 200kb bin is used for detecting copy number variation with abnormal size of more than 4Mb, when preparing the negative sample library, a Y chromosome fragment is used, training data is carried out under a gaussian mixture model, male and female samples are distinguished, autosomes are used as negative references for all samples, different gender groups are used for generating sex chromosome negative references, when a new sample is detected, the gender is automatically predicted, and a correct negative reference library is selected, so that the detection accuracy is improved.
CN202211103951.2A 2022-09-09 2022-09-09 Method for detecting chromosome aneuploidy before embryo implantation Pending CN116606921A (en)

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Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN117174180A (en) * 2023-09-19 2023-12-05 上海品峰医疗科技有限公司 Visualization system for bioinformatics analysis
CN117402961A (en) * 2023-12-13 2024-01-16 北京华宇亿康生物工程技术有限公司 Primer, kit and method for rapidly detecting chromosome aneuploidy before embryo implantation
CN117721222A (en) * 2024-02-07 2024-03-19 北京大学第三医院（北京大学第三临床医学院） Method for predicting embryo implantation by single cell transcriptome and application

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN117174180A (en) * 2023-09-19 2023-12-05 上海品峰医疗科技有限公司 Visualization system for bioinformatics analysis
CN117402961A (en) * 2023-12-13 2024-01-16 北京华宇亿康生物工程技术有限公司 Primer, kit and method for rapidly detecting chromosome aneuploidy before embryo implantation
CN117402961B (en) * 2023-12-13 2024-03-12 北京华宇亿康生物工程技术有限公司 Primer, kit and method for rapidly detecting chromosome aneuploidy before embryo implantation
CN117721222A (en) * 2024-02-07 2024-03-19 北京大学第三医院（北京大学第三临床医学院） Method for predicting embryo implantation by single cell transcriptome and application
CN117721222B (en) * 2024-02-07 2024-05-10 北京大学第三医院（北京大学第三临床医学院） Method for predicting embryo implantation by single cell transcriptome and application

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