Genome-wide Copy Number Variation Polymorphism In Yunnan Normal Population And Its Clinical Application

Object::Copy number variations(CNVs)are structural variations which widely distributed in the human genome.Most CNVs are benign variants,and a few of CNVs are pathogenic variants which could cause mild to severe birth defects.Studies have shown that there are population differences in CNVs polymorphism,and there is no report on the Yunnan population currently.In this study,the previous whole-genome sequencing data was re-analyzed to obtain the CNVs polymorphism of the normal population in Yunnan,that could provide basic human genetic data for prenatal diagnosis and genetic counseling.Method:4661 pregnant women who underwent non-invasive prenatal testing(NIPT)of fetal cell-free DNA in maternal blood from the Department of Medical Genetics of the First People’s Hospital of Yunnan Province from July 2017 to December 2018.Excluded from the abnormal of maternal phenotypes,birth history or the results of test,4532 normal pregnant women were finally screened into the group.The NIPT sequencing data used in this study is a mixture of maternal source(70%-95%)and fetal source(5%-30%).Therefore,we first use Wisecondor X software to filter the interference of fetal source fragments and low ratio of mosaic in the NIPT data,extract the CNVs sourced maternal,and use Bedtools to merge the CNVs to obtain the CNVs spectrum of the normal population in Yunnan;then select the 30 pregnant women’s peripheral blood samples with a higher frequency in the variations spectrum,extracted g DNA from the sample and detect the CNVs with copy number variations sequencing(CNV-seq)technology,which was compared and verified with the CNVs results extracted by the bioinformatics analysis.Finally,Classify CNVs software was used to evaluate the pathogenicity of CNVs,combined with ACMG guidelines,medical genetics databases and literature reports,to discuss and analyze the characteristics of the CNVs spectrum of the normal population in Yunnan.Result:(1)A total of 909 maternal CNVs were extracted from the selected 4,532 pregnant women by NIPT sequencing data with bioinformatics analysis,and 88.62% of the CNVs fragments were in the range of 300 Kb to 1Mb.The population carrying rate of CNVs which fragment length more than 300 Kb was 17.92%(812/4532),of which 88.51% only carried 1 CNVs.Among the CNVs detected,the ratio of duplication and deletion type was 714/195.These CNVs are distributed on22 chromosome and X sex chromosomes,and CNVs on chr7,chr8 and chr X had a larger quantity and covered with a wider range;(2)After merged with the Bedtools software,46 common CNVs in Yunnan normal population(carrying rate 0.0009～0.0092)were obtained.Among them,26 CNVs have a high frequency variation in both Han and ethnic minority groups;12 CNVs have a higher frequency in Han and a lower rate in ethnic minorities;and 8 CNVs have a higher carrier rate in ethnic minorities,a lower in Han;(3)For the selected 30 sample,the CNVs detected by the CNV-seq technology was consistent with the CNVs result re-analyzed the NIPT sequencing data;(4)The pathogenicity assessment of 46 high-frequency CNVs by the Classify CNVs software.Among them,37 CNVs scored 0 points,4 CNVs scored-0.6 points,which are evaluated as variants of unknown significance(VUS);Xp22.31 del,16p13.11 dup and 22q11.21 dup are respectively scored as 1,1.15,and 1.45,which are evaluated as pathogenic.2p23.2-p23.3 dup and 16p11.2-p11.1 dup were scored-1,which was assessed as benign.(5)Among 473 low-frequency CNVs,16p13.11 del,17p12 del/dup,22q11.2 del and Xq28 del were assessed as pathogenic.Conclusion:(1)This study successfully obtained the copy number variation polymorphism spectrum of the normal population in Yunnan.The high-frequency CNVs of Yunnan Han and ethnic minority groups are basically the same,but there are a few differences.(2)The CNVs re-analyzed NIPT data is consistent with the CNV-seq results,which verifies that the CNVs obtained by reanalysis is reliable.(3)Among the CNVs with high ratio of carrier in Yunnan population detected in this study,90% CNVs with a fragment <1Mb,usually inherited from parents and has less clinical effect.It is immature to use the scoring value to determine the function of the small segment CNVs mechanically for it would judge the benign and likely benign CNVs as VUS CNVs wrongly.(4)In this study,we discovered the carrier rate of Xp22.31 del in Yunnan pregnant women was 17.7/10,000.This CNV associated X-linked ichthyosis and occurred only in males,and the incidence rate in Yunnan male newborns is 9/10,000.At the same time,the population carrying rates of 16p13.11 dup and 22q11.2 dup are 22/10,000 and 13/10,000.The two CNVs both have penetrance incompleteness and clinical heterogeneity.The pathogenicity of the two needs more discussion.(5)Low-frequency CNVs in Yunnan population did not means safe.Among them,rare CNVs are related to 22q11.2 deletion syndrome(DGS),16p13.11 del,17p12del/dup and Xq28 del pathogenic CNVs.