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zCall: a rare variant caller for array-based genotyping

Jacqueline I. Goldstein, Andrew Crenshaw, Jason Carey, George B. Grant, Jared Maguire, Menachem Fromer, Colm O'Dushlaine, Jennifer L. Moran, Kimberly Chambert, Christine Stevens, Pamela Sklar, Christina M. Hultman (+5 others)
<span title="2012-07-27">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
zCall is a variant caller specifically designed for calling rare single-nucleotide polymorphisms from array-based technology.  ...  We demonstrate improved detection of rare alleles when applying zCall to samples that have both Illumina Infinium HumanExome BeadChip and exome sequencing data available.  ...  ACKNOWLEDGEMENTS We thank the Genetic Analysis Platform, the Biological Samples Platform and the Genome Sequencing Platform at the Broad Institute for data generation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts479">doi:10.1093/bioinformatics/bts479</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22843986">pmid:22843986</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3463112/">pmcid:PMC3463112</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vcpatnt7sfgnhdrpk3evtghjhq">fatcat:vcpatnt7sfgnhdrpk3evtghjhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200502104435/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3463112&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c2/0f/c20f6610550fd4c8ecf84b194c34741d68774b22.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts479"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463112" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Illumina human exome genotyping array clustering and quality control

Yan Guo, Jing He, Shilin Zhao, Hui Wu, Xue Zhong, Quanhu Sheng, David C Samuels, Yu Shyr, Jirong Long
<span title="2014-10-16">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/z2jd6b73erhgxdr3pwdyqxtsta" style="color: black;">Nature Protocols</a> </i> &nbsp;
Researchers have struggled to generate a reliable protocol for processing exome genotyping array data.  ...  exome genotyping array targets the exome plus rare single-nucleotide polymorphisms (SNPs), a feature that makes it substantially more challenging to process than previous genotyping arrays that targeted  ...  (P30 CA068485) and R01CA158473. We thank M. Bjoring for editorial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nprot.2014.174">doi:10.1038/nprot.2014.174</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25321409">pmid:25321409</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4441213/">pmcid:PMC4441213</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qqupmutlu5boficgj7reooons4">fatcat:qqupmutlu5boficgj7reooons4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191027010327/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4441213&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/eb/f0/ebf05ca9e13d0668e721955a61107171b2c6f766.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nprot.2014.174"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441213" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The rate of false polymorphisms introduced when imputing genotypes from global imputation panels [article]

Ida Surakka, Antti-Pekka Sarin, Sanni E Ruotsalainen, Richard Durbin, Veikko Salomaa, Mark Daly, Aarno Palotie, Samuli Ripatti
<span title="2016-10-13">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
project Phase I3; 1000G) and compare the results to a Finnish population-specific reference panel combining whole genome and exome sequenced samples.  ...  In this study we evaluate the rate of false positive variants introduced by the imputation of Finnish genotype data using global reference panels (Haplotype Reference Consortium1; HRC, and the 1000Genomes  ...  ., et al. zCall: a rare variant caller for array-based genotyping: genetics and population analysis. Bioinformatics 28, 2543-2545 (2012) 15. Delaneau, O., Zagury, J. F. and Marchini, J.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/080770">doi:10.1101/080770</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4r4zi7ia4zbb5kmb3mzrvzhd7m">fatcat:4r4zi7ia4zbb5kmb3mzrvzhd7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430144818/https://www.biorxiv.org/content/biorxiv/early/2016/10/13/080770.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d7/34/d734909239ada9708c4eb367a9668821499350aa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/080770"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Best Practices and Joint Calling of the HumanExome BeadChip: The CHARGE Consortium

Megan L. Grove, Bing Yu, Barbara J. Cochran, Talin Haritunians, Joshua C. Bis, Kent D. Taylor, Mark Hansen, Ingrid B. Borecki, L. Adrienne Cupples, Myriam Fornage, Vilmundur Gudnason, Tamara B. Harris (+19 others)
<span title="2013-07-12">2013</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Genotyping arrays are a cost effective approach when typing previously-identified genetic polymorphisms in large numbers of samples.  ...  One limitation of genotyping arrays with rare variants (e.g., minor allele frequency [MAF] ,0.01) is the difficulty that automated clustering algorithms have to accurately detect and assign genotype calls  ...  We would also like to recognize the following individuals at UT for their expertise and participation in the genotype calling, data management and analyses, respectively: Irina Strelets, Genesis Williams  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0068095">doi:10.1371/journal.pone.0068095</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23874508">pmid:23874508</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3709915/">pmcid:PMC3709915</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6xfzp2njofc6pmeozxvnaihup4">fatcat:6xfzp2njofc6pmeozxvnaihup4</a> </span>
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Meta-GWAS and Meta-Analysis of Exome Array Studies Do Not Reveal Genetic Determinants of Serum Hepcidin

Tessel E. Galesloot, Niek Verweij, Michela Traglia, Caterina Barbieri, Freerk van Dijk, Anneke J. Geurts-Moespot, Domenico Girelli, Lambertus A. L. M. Kiemeney, Fred C. G. J. Sweep, Morris A. Swertz, Peter van der Meer, Clara Camaschella (+5 others)
<span title="2016-11-15">2016</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
We studied the association of common and rare single nucleotide variants (SNVs) with serum hepcidin in one Italian study and two large Dutch population-based studies.  ...  In addition, we encourage follow-up of the potentially interesting genes that resulted from the gene-based analysis of low-frequency and rare variants.  ...  Genotype data were called with the default genotype caller in Genome Studio and uncalled genotypes were recalled using the zCall algorithm, which is specifically designed for calling rare variants [39  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0166628">doi:10.1371/journal.pone.0166628</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27846281">pmid:27846281</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5112847/">pmcid:PMC5112847</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/24susj7c5jacjnwz3if2lclkqi">fatcat:24susj7c5jacjnwz3if2lclkqi</a> </span>
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Protective coding variants inCFHandPELI3and a variant nearCTRB1are associated with age-related macular degeneration†

Yi Yu, Erin K. Wagner, Eric H. Souied, Sanna Seitsonen, Ilkka J. Immonen, Paavo Häppölä, Soumya Raychaudhuri, Mark J. Daly, Johanna M. Seddon
<span title="2016-12-22">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b6edj2e2zzf77igiepykq3vzii" style="color: black;">Human Molecular Genetics</a> </i> &nbsp;
common variants using logistic regression, adjusting for genetic ancestry based on principal component analysis, analyzing the samples from the Boston, French and Finnish cohorts separately and then performed  ...  We performed meta-analyses to identify associations with common variants and performed single variant and gene-based burden tests to identify associations with rare variants.  ...  The copyright holder for this preprint (which was not .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/hmg/ddw336">doi:10.1093/hmg/ddw336</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28011711">pmid:28011711</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6078639/">pmcid:PMC6078639</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2h2kl7uxnjhqpnqwst6ftpdqqe">fatcat:2h2kl7uxnjhqpnqwst6ftpdqqe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220120605/http://pdfs.semanticscholar.org/2816/196da23f7e0782b89940f7b0a6a0672fb882.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/28/16/2816196da23f7e0782b89940f7b0a6a0672fb882.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/hmg/ddw336"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078639" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Novel protective associations with age-related macular degeneration: A common variant nearCTRB1and a rare variant inPELI3 [article]

Erin K Wagner, Yi Yu, Eric H Souied, Sanna Seitsonen, Ilkka J Immonen, Paavo Häppölä, Soumya Raychaudhuri, Mark J Daly, Johanna M. Seddon
<span title="2015-12-11">2015</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We performed meta-analyses to identify associations with common variants and performed single variant and gene-based burden tests to identify associations with rare variants.  ...  We genotyped 4,332 cases and 25,268 controls of European ancestry from three different populations using the Illumina Infinium HumanExome BeadChip.  ...  We thank the numerous ophthalmologists throughout the United States that contributed to the Boston AMD cohort, the ophthalmologists from the Clinical Researches Functional Unit, CHI Créteil, France, and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/034173">doi:10.1101/034173</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q3djvd64j5cgnpdhzt4rjaywvu">fatcat:q3djvd64j5cgnpdhzt4rjaywvu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502125413/https://www.biorxiv.org/content/biorxiv/early/2016/04/09/034173.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/24/05/24059ebdf5f3135d61dab35e6855d30a510b47a3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/034173"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Independent Replication and Meta-Analysis for Endometriosis Risk Loci

Yadav Sapkota, Amelie Fassbender, Lisa Bowdler, Jenny N. Fung, Daniëlle Peterse, Dorien O, Grant W. Montgomery, Dale R. Nyholt, Thomas M. D'Hooghe
<span title="2015-09-04">2015</span> <i title="Cambridge University Press (CUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/u7my2wkygjamrjaxyx22iv3kuq" style="color: black;">Twin Research and Human Genetics</a> </i> &nbsp;
Meta-analysis with the published results yields genome-wide significant evidence for rs7521902, rs13394619, rs6542095, rs12700667, rs7739264, and rs1537377.  ...  Overall, this study provides important replication in a uniquely characterized independent population, and indicates that the majority of the original genome-wide association findings are not due to chance  ...  Acknowledgements We would like to all the participants in the endometriosis studies that are included in this analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/thg.2015.61">doi:10.1017/thg.2015.61</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26337243">pmid:26337243</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/arr2j3buxrhrredxcjh73pfeuy">fatcat:arr2j3buxrhrredxcjh73pfeuy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190324110759/https://core.ac.uk/download/pdf/33505712.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/76/ea/76ea64004b95b8c251680d2e98cb35de15a33611.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/thg.2015.61"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> cambridge.org </button> </a>

Novel Genetic Loci Associated With Retinal Microvascular DiameterCLINICAL PERSPECTIVE

Richard A. Jensen, Xueling Sim, Albert Vernon Smith, Xiaohui Li, Jóhanna Jakobsdóttir, Ching-Yu Cheng, Jennifer A. Brody, Mary Frances Cotch, Barbara Mcknight, Ronald Klein, Jie Jin Wang, Annette Kifley (+21 others)
<span title="2015-11-13">2015</span> <i title="Ovid Technologies (Wolters Kluwer Health)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jp4g3aaxsvhyfje2ubfvxttz24" style="color: black;">Circulation: Cardiovascular Genetics</a> </i> &nbsp;
Goldstein JI, Crenshaw A, Carey J, Grant GB, Maguire J, Fromer M, et al; Swedish Schizophrenia Consortium; ARRA Autism Sequencing Consortium. zCall: a rare variant caller for array-based genotyping: genetics  ...  or zCall 38 was used for genotype calling.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1161/circgenetics.115.001142">doi:10.1161/circgenetics.115.001142</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26567291">pmid:26567291</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4758888/">pmcid:PMC4758888</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/evjsh63safh2xl3tskl54xl6fi">fatcat:evjsh63safh2xl3tskl54xl6fi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721000715/http://circgenetics.ahajournals.org/content/circcvg/9/1/45.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ab/fa/abfa9b03f5f4b5bf49161b6925ff34867e2bc627.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1161/circgenetics.115.001142"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758888" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-Wide Association of Heroin Dependence in Han Chinese

Gursharan Kalsi, Jack Euesden, Jonathan R. I. Coleman, Francesca Ducci, Fazil Aliev, Stephen J. Newhouse, Xiehe Liu, Xiaohong Ma, Yingcheng Wang, David A. Collier, Philip Asherson, Tao Li (+2 others)
<span title="2016-12-09">2016</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Gene-based association analysis identified genome-wide significant association between variants in CCDC42 and heroin addiction.  ...  Analysis using the diagnostic criteria of heroin dependence yielded suggestive evidence for association between variants in the genes CCDC42 (coiled coil domain 42; p = 2.8x10 -7 ) and BRSK2 (BR serine  ...  We express gratitude to Dr Joel Gelernter and Dr Richard Sherva for providing the use of summary statistics of their published study on opioid dependence, to enable us to perform in silico replication  ... 
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