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The Biological Significance of multi-copy Regions and Their Impact on Variant Discovery

Genomics, Proteomics & Bioinformatics 2020年第5期18卷 516-524页

作者： Jing Sun Yanfang Zhang Minhui Wang Qian Guan Xiujia Yang Jin Xia Ou Mingchen Yan Chengrui Wang Yan Zhang Zhi-Hao Li Chunhong Lan Chen Mao Hong-Wei Zhou Bingtao Hao Zhenhai Zhang State Key Laboratory of Organ Failure Research National Clinical Research Center for Kidney DiseaseDivision of NephrologyNanfang HospitalSouthern Medical UniversityGuangzhou 510515China Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China Key Laboratory of Mental Health of the Ministry of Education Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired IntelligenceSouthern Medical UniversityGuangzhou 510515China Center for Precision Medicine Shunde Hospital of Southern Medical UniversityFoshan 528399China Microbiome Medicine Center Division of Laboratory MedicineZhujiang HospitalSouthern Medical UniversityGuangzhou 510282China Division of Epidemiology School of Public HealthSouthern Medical UniversityGuangzhou 510515China

Identification of genetic variants via high-throughput sequencing(HTS)technologies has been essential for both fundamental and clinical ***,to what extent the genome sequence composition affects variant calling remains *** this study,we identified 63,897 multi-copy sequences(MCSs)with a minimum length of 300 bp,each of which occurs at least twice in the human *** 151,749 genomic loci(multi-copy regions,or MCRs)harboring these MCSs account for 1.98% of the genome and are distributed unevenly across *** containing the same MCS tend to be located on the same *** Ontology(GO)analyses revealed that 3800 genes whose UTRs or exons overlap with MCRs are enriched for Golgirelated cellular component terms and various enzymatic activities in the GO biological function *** are also enriched for loci that are sensitive to neocarzinostatin-induced double-strand ***,genetic variants discovered by genome-wide association studies and recorded in dbSNP are significantly underrepresented in *** simulated HTS datasets,we show that false variant discovery rates are significantly higher in MCRs than in other genomic *** results suggest that extra caution must be taken when identifying genetic variants in the MCRs via HTS technologies.

关键词： multi-copy sequence multi-copy region Genetic study Variant discovery High-throughput sequencing

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