GenoPipe: identifying the genotype of origin within (epi)genomic datasets.
GenoPipe: identifying the genotype of origin within (epi)genomic datasets.
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DOI：
10.1093/nar/gkad950
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发表时间：
2023-12-11
影响因子：
14.9
通讯作者：
Lai, William K. M.
中科院分区：
文献类型：
--
作者：
Lang, Olivia W.;Srivastava, Divyanshi;Pugh, B. Franklin;Lai, William K. M.
对实验结果的信心是发现的关键。随着基因组学数据生成的规模呈指数级增长，尽管许多实验室尽了最大努力，但实验误差可能会保持同步。技术错误可能并且确实发生在基因组学测定的几乎每个阶段（即细胞系污染、试剂交换、试管错误标记等）。并且在执行后通常难以识别。然而，在基因组实验中测序的DNA含有编码在其中的某些标志物（例如插入缺失），并且通常可以从实验数据集在法医学上确定。我们开发了Genotype validation Pipeline（GenoPipe），这是一套启发式工具，可直接对来自单个高通量测序实验的原始和比对测序数据进行操作，以表征源材料的基础基因组。我们演示了GenoPipe如何通过识别生物体基因组固有的独特标记（即表位插入，基因缺失和SNP）来验证和挽救错误注释的实验。
Confidence in experimental results is critical for discovery. As the scale of data generation in genomics has grown exponentially, experimental error has likely kept pace despite the best efforts of many laboratories. Technical mistakes can and do occur at nearly every stage of a genomics assay (i.e. cell line contamination, reagent swapping, tube mislabelling, etc.) and are often difficult to identify post-execution. However, the DNA sequenced in genomic experiments contains certain markers (e.g. indels) encoded within and can often be ascertained forensically from experimental datasets. We developed the Genotype validation Pipeline (GenoPipe), a suite of heuristic tools that operate together directly on raw and aligned sequencing data from individual high-throughput sequencing experiments to characterize the underlying genome of the source material. We demonstrate how GenoPipe validates and rescues erroneously annotated experiments by identifying unique markers inherent to an organism's genome (i.e. epitope insertions, gene deletions and SNPs).
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DOI：
10.1016/j.atg.2016.06.001
发表时间：
2016-09
期刊：
Applied & translational genomics
影响因子：
--
作者：
Endrullat, Christoph;Glokler, Jorn;Franke, Philipp;Frohme, Marcus
通讯作者：
Frohme, Marcus
影响因子：
64.8
作者：
Harris CR;Millman KJ;van der Walt SJ;Gommers R;Virtanen P;Cournapeau D;Wieser E;Taylor J;Berg S;Smith NJ;Kern R;Picus M;Hoyer S;van Kerkwijk MH;Brett M;Haldane A;Del Río JF;Wiebe M;Peterson P;Gérard-Marchant P;Sheppard K;Reddy T;Weckesser W;Abbasi H;Gohlke C;Oliphant TE
通讯作者：
Oliphant TE
影响因子：
3.7
作者：
Horbach SPJM;Halffman W
通讯作者：
Halffman W
影响因子：
8.8
作者：
Bosque A;Nilson KA;Macedo AB;Spivak AM;Archin NM;Van Wagoner RM;Martins LJ;Novis CL;Szaniawski MA;Ireland CM;Margolis DM;Price DH;Planelles V
通讯作者：
Planelles V
影响因子：
11.4
作者：
de Jonge, Wim J.;O'Duibhir, Eoghan;Holstege, Frank C. P.
通讯作者：
Holstege, Frank C. P.