Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases.

Tópicos

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{ imag(2675) segment(2577) method(1081) }
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{ data(3963) clinic(1234) research(1004) }
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{ patient(2837) hospit(1953) medic(668) }
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{ patient(1821) servic(1111) care(1106) }
{ can(981) present(881) function(850) }
{ high(1669) rate(1365) level(1280) }
{ result(1111) use(1088) new(759) }
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{ analysi(2126) use(1163) compon(1037) }
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{ use(1733) differ(960) four(931) }
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{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

Repetitive and redundant regions of a genome are particularly problematic for mapping sequencing reads. In the present paper, we compile a list of the unmappable regions in the human genome based on the following definition: hypothetical reads with length 1 kb which cannot be uniquely mapped with zero-mismatch alignment for the described regions, considering both the forward and reverse strand. The respective collection of unmappable regions covers 0.77% of the sequence of human autosomes and 8.25% of the sex chromosomes in the reference genome GRCh37/hg19 (overall 1.23%). Not surprisingly, our unmappable regions overlap greatly with segmental duplication, transposable elements, and structural variants. About 99.8% of bases in our unmappable regions are part of either segmental duplication or transposable elements and 98.3% overlap structural variant annotations. Notably, some of these regions overlap units with important biological functions, including 4% of protein-coding genes. In contrast, these regions have zero intersection with the ultraconserved elements, very low overlap with microRNAs, tRNAs, pseudogenes, CpG islands, tandem repeats, microsatellites, sensitive non-coding regions, and the mapping blacklist regions from the ENCODE project.

Resumo Limpo

repetit redund region genom particular problemat map sequenc read present paper compil list unmapp region human genom base follow definit hypothet read length kb uniqu map zeromismatch align describ region consid forward revers strand respect collect unmapp region cover sequenc human autosom sex chromosom refer genom grchhg overal surpris unmapp region overlap great segment duplic transpos element structur variant base unmapp region part either segment duplic transpos element overlap structur variant annot notabl region overlap unit import biolog function includ proteincod gene contrast region zero intersect ultraconserv element low overlap microrna trnas pseudogen cpg island tandem repeat microsatellit sensit noncod region map blacklist region encod project

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