Establishment Of Balanced Chromosomal Rearrangements Detection Based On Low-pass Whole Genome Sequencing

Miscarriage is one of the most common pregnancy complications.Recurrent miscarriage is two or more consecutive pregnancy losses.The incidence of miscarriage is as high as 10%-15% of the total number of pregnancies,80% of which are early miscarriage.Numerous researches have reported that chromosomal abnormalities are critical to this particular phenotype.Chromosomal abnormalities are mainly divided into numerical abnormal and structural abnormal.Numerical abnormal consist of trisomy(such as trisomy 13,trisomy 18 and trisomy 21),triploid and X monomer,etc.Structural abnormalities contain chromosomal translocation and chromosomal inversion,etc.Balanced chromosomal rearrangement is a type of chromosomal structural variant without cytogenetically apparent gain or loss of chromatin.Phenotypically normal carriers are at risk for reproductive problems such as recurrent miscarriage.Conventional karyotyping,the gold standard for balanced chromosomal rearrangement detection,has limitations for detecting balanced chromosomal rearrangement accurately.This study utilizes pair-end low-pass whole genome sequencing library construction and sequencing,based on the bioinformation analysis for sequencing data,which can make the breakpoints of balanced chromosomal rearrangement reaches single base resolution,thereby it can break the limitations of traditional detection methods and providing more accurate results for clinical interpretation.The results of this study showed below:1.In this study,4 chromosomal translocations were detected in samples from 1000 human genomes,sample HG02260,HG03729,NA18612 and NA20764 comes from Peruvian(Americas),Telugu(South Asia),Chinese(East Asia)and Tuscan(Europe)respectively.The translocations between the long arm of chromosome 9 and the long arm of chromosome 14,the long arm of chromosome 3 and the short arm of chromosome 17,the long arm of chromosome 16 and the length of chromosome 17 and the short arm of chromosome 2 and the short arm of chromosome 19 were detected in sample HG02260,HG03729,NA18612 and NA20764 respectively.2.At the same time,four inversion samples were detected in the 1000 human genomes,sample NA20759,HG04152,NA18959 and NA21133 comes from Tuscan(Europe),Bangladeshi(South Asia),Japanese(East Asia)and Gujarat(South Asia)respectively.A 13 MB inversion was detected in the short arm of chromosome 2 of NA20758,another 4MB inversion was detected in the long arm of chromosome 1 of HG04152,a small 217 KB inversion was detected in the long arm of chromosome 3 of NA18959,and an inversion about 58 KB was detected in the short arm of the X chromosome of NA21133.3.In this study,the cell lines of these 8 samples were obtained from the Coriell Institute,but three of the four inversions were less than 5 MB(HG04152,NA18959,NA21133).Therefore,these three samples have no need to performed the G-banding karyotype.G-banding karyotype analysis was performed on the cell lines of the five samples(HG02260,HG03729,NA18612,NA20764 and NA20759).The results were consistent with the results of low-pass whole genome sequencing.The translocations and inversions had been validated in 1000 human genomes successfully.4.In this study,77 recurrent miscarriages samples with G-banding karyotype results were collected.The results of these samples were compared with G-banding karyotype after DNA quality control,library construction,sequencing and bioinformatics analysis.It was found that 59 of the 77 low-pass whole genome sequencing results were consistent with the G-band karyotype analysis results;Among 10 of the 77 samples,the low-pass whole genome sequencing results were normal,while the G-band karyotype analysis was abnormal;The remaining 8 cases were abnormal in low-pass whole genome sequencing results,but their Gband karyotype results were normal.Overall,most of the samples(59/77 = 76.62%)were consistent between the low-pass whole genome sequencing results and G-band karyotype results,suggesting that low-pass whole genome sequencing has the potential to replace traditional methods.In a word,with the sequencing techniques development and progress in the future,the length of sequencing will be prolonged,and then the shortcomings of the current sequencing technology will be improved,and finally the low-pass whole genome sequencing probably replace the G-banding karyotype analysis as the new gold standard.