vamos: variable-number tandem repeats annotation using efficient motif sets

被引：9
|
作者：
Ren, Jingwen [1 ]
Gu, Bida [1 ]
Chaisson, Mark J. P. [1 ]
机构：
[1] Univ Southern Calif, Dept Quantitat & Computat Biol, Los Angeles, CA 90007 USA
来源：
GENOME BIOLOGY | 2023年 / 24卷 / 01期
基金：
美国国家卫生研究院;
关键词：
Variable-number tandem repeats; Long-read sequencing; Motif composition; HUMAN GENOME; COPY NUMBER; SEQUENCE;
D O I：
10.1186/s13059-023-03010-y
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
Roughly 3% of the human genome is composed of variable-number tandem repeats (VNTRs): arrays of motifs at least six bases. These loci are highly polymorphic, yet current approaches that define and merge variants based on alignment breakpoints do not capture their full diversity. Here we present a method vamos: VNTR Annotation using efficient Motif Sets that instead annotates VNTR using repeat composition under different levels of motif diversity. Using vamos we estimate 7.4-16.7 alleles per locus when applied to 74 haplotype-resolved human assemblies, compared to breakpoint-based approaches that estimate 4.0-5.5 alleles per locus.
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页数：18
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