Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
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DOI：
10.1111/1755-0998.13300
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发表时间：
2020-12-19
影响因子：
7.7
通讯作者：
Lizano, Esther
中科院分区：
文献类型：
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作者：
Fontsere, Claudia;Alvarez-Estape, Marina;Lizano, Esther
作为DNA来源的非侵入性样品在濒危物种的基因组研究中越来越受到关注。然而，它们的复杂性和低内源DNA含量阻碍了高质量数据的恢复。靶捕获已成为一种有效的方法，以丰富的内源性部分的非侵入性样品，如粪便，但其灵敏度尚未得到广泛的研究。处理内源性DNA含量低于1%的粪便样本是一个常见的问题，当事先从大量收集的样本是不可能的。然而，被归类为不利于靶捕获测序的样本可能是唯一特定地理位置的唯一代表，或回答感兴趣的问题。为了探索如何在不重复DNA提取和产生新文库的情况下增加文库复杂性，在这项研究中，我们使用内源性含量比例非常低的粪便样品捕获了60只黑猩猩（Pan troglodytes）的外显子组（
Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (