Long-read trio sequencing of individuals with unsolved intellectual disability.
Long-read trio sequencing of individuals with unsolved intellectual disability.
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DOI：
10.1038/s41431-020-00770-0
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发表时间：
2021-04
期刊：
影响因子：
--
通讯作者：
Gilissen C
中科院分区：
文献类型：
--
作者：
Pauper M;Kucuk E;Wenger AM;Chakraborty S;Baybayan P;Kwint M;van der Sanden B;Nelen MR;Derks R;Brunner HG;Hoischen A;Vissers LELM;Gilissen C
长读段测序（LRS）有可能全面识别所有医学相关的基因组变异，包括短读段测序（SRS）方法通常遗漏的变异。为了确定这一潜力，我们使用Pacific Biosciences Sequel I系统对5个三联体进行了约15×-40×基因组覆盖的LRS。各自的先证者被诊断为智力残疾（ID），其病因在SRS外显子组和基因组后仍未得到解决。LRS覆盖率的系统评估显示，约35 Mb的人类参考基因组仅可通过LRS而非SRS访问。全基因组结构变异（SV）调用平均每个个体产生28，292个SV调用，总计12.9 Mb序列。允许研究分离的基于Trio的分析显示，在整个基因组中，高达95%的这些SV调用具有一致性，并且80%的LRS SV调用未被SRS识别。从头突变分析未发现任何从头SV，证实这些是罕见事件。由于高序列覆盖率，我们也能够调用单核苷酸替换。平均而言，我们发现每个基因组有300万个替换，孟德尔遗传一致性高达97%。其中，约100，000个位于仅由LRS捕获的基因组的约35 Mb中。此外，这些变异影响了64个基因的编码序列，包括32个已知的孟德尔疾病基因。我们的数据显示，与SRS相比，LRS在识别医学相关基因组变异方面具有潜在的附加值。
Long-read sequencing (LRS) has the potential to comprehensively identify all medically relevant genome variation, including variation commonly missed by short-read sequencing (SRS) approaches. To determine this potential, we performed LRS around 15×–40× genome coverage using the Pacific Biosciences Sequel I System for five trios. The respective probands were diagnosed with intellectual disability (ID) whose etiology remained unresolved after SRS exomes and genomes. Systematic assessment of LRS coverage showed that ~35 Mb of the human reference genome was only accessible by LRS and not SRS. Genome-wide structural variant (SV) calling yielded on average 28,292 SV calls per individual, totaling 12.9 Mb of sequence. Trio-based analyses which allowed to study segregation, showed concordance for up to 95% of these SV calls across the genome, and 80% of the LRS SV calls were not identified by SRS. De novo mutation analysis did not identify any de novo SVs, confirming that these are rare events. Because of high sequence coverage, we were also able to call single nucleotide substitutions. On average, we identified 3 million substitutions per genome, with a Mendelian inheritance concordance of up to 97%. Of these, ~100,000 were located in the ~35 Mb of the genome that was only captured by LRS. Moreover, these variants affected the coding sequence of 64 genes, including 32 known Mendelian disease genes. Our data show the potential added value of LRS compared to SRS for identifying medically relevant genome variation.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
7
作者：
Huddleston J;Chaisson MJP;Steinberg KM;Warren W;Hoekzema K;Gordon D;Graves-Lindsay TA;Munson KM;Kronenberg ZN;Vives L;Peluso P;Boitano M;Chin CS;Korlach J;Wilson RK;Eichler EE
通讯作者：
Eichler EE
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
--
作者：
Pilipenko, Valentina V;He, Hua;Martin, Lisa J
通讯作者：
Martin, Lisa J
影响因子：
30.8
作者：
Cooper, Gregory M.;Zerr, Troy;Kidd, Jeffrey M.;Eichler, Evan E.;Nickerson, Deborah A.
通讯作者：
Nickerson, Deborah A.