OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data

Zhu, Pengyuan; He, Lingyu; Li, Yaqiao; Huang, Wenpan; Feng, Xiaobing; Lin, Lin; Zhi, Qihuan; Zhang, Wenwei; Tang, Y. Tom; Geng, Chunyu; Lǚ, Zhiyuan; Xu, Xun

doi:10.1371/journal.pone.0097507

Cited by 36 publications

(20 citation statements)

References 18 publications

(18 reference statements)

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“…Read files (Fastq) were generated from the sequencing platform via the manufacturer’s proprietary software. Reads were mapped using the Burrows-Wheeler Aligner 48 and local realignment of the mapped reads around potential insertion/deletion (indel) sites was carried out with the GATK version 1.6 49 . Duplicate reads were marked using Picard version 1.62 (http://picard.sourceforge.net).…”

Section: Methodsmentioning

confidence: 99%

An ancient protein-DNA interaction underlying metazoan sex determination

Murphy

Lee

Rojo

et al. 2015

Nat Struct Mol Biol

101

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DMRT transcription factors are deeply conserved regulators of metazoan sexual development. They share the DM DNA binding domain, a unique intertwined double zinc-binding module followed by a C-terminal recognition helix, which binds to a pseudopalindromic target DNA. Here we show that DMRT proteins employ a unique binding interaction, inserting two adjacent antiparallel recognition helices into a widened DNA major groove to make base-specific contacts. Versatility in how specific base contacts are made allows human DMRT1 to employ multiple DNA binding modes (tetramer, trimer, dimer). ChIP-Exo indicates that multiple DNA binding modes also are used in vivo. We show that mutations affecting residues crucial for DNA recognition are associated with an intersex phenotype in flies and in male-to-female sex reversal in humans. Our results illuminate an ancient molecular interaction that underlies much of metazoan sexual development.

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Section: Methodsmentioning

confidence: 99%

An ancient protein-DNA interaction underlying metazoan sex determination

Murphy

Lee

Rojo

et al. 2015

Nat Struct Mol Biol

101

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“…Read sequences were aligned to a mouse reference genome. The exome single nucleotide polymorphism (SNP) calls were produced with the GATK SNP calling pipeline [ 48 ]. Variant annotation was conducted with snpEff to add information, such as the name of the gene that harbored the variant, the effect of the mutation (missense variant, synonymous variant, etc.…”

Section: Methodsmentioning

confidence: 99%

Dual oncogenic and tumor suppressor roles of the promyelocytic leukemia gene in hepatocarcinogenesis associated with hepatitis B virus surface antigen

Chung

2016

Oncotarget

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Proteasome-mediated degradation of promyelocytic leukemia tumor suppressor (PML) is upregulated in many viral infections and cancers. We previously showed that PML knockdown promotes early-onset hepatocellular carcinoma (HCC) in hepatitis B virus surface antigen (HBsAg)-transgenic mice. Here we report the effects of PML restoration on late-onset HBsAg-induced HCC. We compared protein expression patterns, genetic mutations and the effects of pharmacologically targeting PML in wild-type, PML−/−, PML+/+HBsAgtg/o and PML−/−HBsAgtg/o mice. PML−/− mice exhibited somatic mutations in DNA repair genes and developed severe steatosis and proliferative disorders, but not HCC. PML−/−HBsAgtg/o mice exhibited early mutations in cancer driver genes and developed hyperplasia, fatty livers and indolent adipose-like HCC. In PML+/+HBsAg-transgenic mice, HBsAg expression declined over time, and HBsAg-associated PML suppression was concomitantly relieved. Nevertheless, these mice accumulated mutations in genes contributing to oxidative stress pathways and developed aggressive late-onset angiogenic trabecular HCC. PML inhibition using non-toxic doses of arsenic trioxide selectively killed long-term HBsAg-affected liver cells in PML+/+HBsAgtg/o mice with falling HBsAg and rising PML levels, but not normal liver cells or early-onset HCC cells in PML−/−HBsAgtg/0 mice. These findings suggest dual roles for PML as a tumor-suppressor lost in early-onset HBsAg-induced hepatocarcinogenesis and as an oncogenic promoter in late-onset HBsAg-related HCC progression.

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“…Variants were called using the OTG-snpcaller pipeline, which has been reported to map a higher proportion of sequencing reads to the reference genome in comparison to other methods and result in lower error rates when analyzing sequences coming from the PGM platform (Zhu et al 2014). Unlike other sequencing software and pipelines such as the Genome Analysis Toolkit (GATK) and FreeBayes (McKenna et al 2010; Garrison and Marth 2012), OTG-snpcaller is specifically designed to take into account errors associated with PGM data, such as errors around homopolymers, thus increasing overall accuracy.…”

Section: Methodsmentioning

confidence: 99%

KBG syndrome involving a single-nucleotide duplication in ANKRD11

Kleyner

Malcolmson

Tegay

et al. 2016

Cold Spring Harb Mol Case Stud

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KBG syndrome is a rare autosomal dominant genetic condition characterized by neurological involvement and distinct facial, hand, and skeletal features. More than 70 cases have been reported; however, it is likely that KBG syndrome is underdiagnosed because of lack of comprehensive characterization of the heterogeneous phenotypic features. We describe the clinical manifestations in a male currently 13 years of age, who exhibited symptoms including epilepsy, severe developmental delay, distinct facial features, and hand anomalies, without a positive genetic diagnosis. Subsequent exome sequencing identified a novel de novo heterozygous single base pair duplication (c.6015dupA) in ANKRD11, which was validated by Sanger sequencing. This single-nucleotide duplication is predicted to lead to a premature stop codon and loss of function in ANKRD11, thereby implicating it as contributing to the proband's symptoms and yielding a molecular diagnosis of KBG syndrome. Before molecular diagnosis, this syndrome was not recognized in the proband, as several key features of the disorder were mild and were not recognized by clinicians, further supporting the concept of variable expressivity in many disorders. Although a diagnosis of cerebral folate deficiency has also been given, its significance for the proband's condition remains uncertain.

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OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data

Cited by 36 publications

References 18 publications

An ancient protein-DNA interaction underlying metazoan sex determination

An ancient protein-DNA interaction underlying metazoan sex determination

Dual oncogenic and tumor suppressor roles of the promyelocytic leukemia gene in hepatocarcinogenesis associated with hepatitis B virus surface antigen

KBG syndrome involving a single-nucleotide duplication in ANKRD11

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