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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-. </p></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/helpsnpfaq/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-helpsnpfaq-lrg.png" alt="Cover of SNP FAQ Archive" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>SNP FAQ Archive [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK573474_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK573474_dtls__"><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 2005-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/helpsnpfaq/">Contents</a></li></ul></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpsnpfaq/Cnt_Associat_Studies/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpsnpfaq/Cnt_Auto_SNP_Collect/" title="Next page in this title">Next ></a></div></div></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK573474_"><span class="title" itemprop="name">Ascertainment Bias</span></h1><p class="small">Created: <span itemprop="datePublished">July 23, 2005</span>; Last Update: <span itemprop="dateModified">February 18, 2014</span>.</p><p><em>Estimated reading time: 1 minute</em></p></div><div class="body-content whole_rhythm" itemprop="text"><div><h4 id="Cnt_Ascertmnt_Bias.what_is_ascertainment">What is ascertainment bias, and how does it relate to the calculation of SNP frequencies?</h4><blockquote><p>Ascertainment bias is a term in population genetics that describes systematic deviations from an expected theoretical result attributable to the sampling processes used to find (ascertain) SNPs and measure (estimate) their population-specific allele frequencies.</p><p>The distribution of SNP "derived" allele frequency ranges in nature from 1/2N (i.e., one mutant chromosome in the entire species gene pool), to 2N-1/2N (i.e., only one chromosome left in the species gene pool to represent the "ancestral" allelic state; all other chromosomes have the derived allele). This distribution, however, is imperfectly measured when finite sub-samples are drawn from the population. The smaller the finite sample used in our SNP detection (sampling) process, the more “imperfect” the fit between the distribution of derived allele frequencies and the “true” distribution in nature. Here is a graph that illustrates the bias:</p><p>
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</p><p>Modified from Fig.2, Ref. (<a href="#Cnt_Ascertmnt_Bias.References">1</a>).</p><p>If SNPs in dbSNP are ascertained in samples of a few chromosomes, then a fraction of those SNPs will be excessively common in the population relative to potentially larger samples of the same genomic sequence.</p><p>Experimental validation typically means observing the SNP in additional samples unrelated to the original set of chromosomes surveyed to define the SNP. Therefore, common SNPs will “validate” with a higher rate than SNPs with a really rare minor allele, because larger samples are needed to recapture (and hence confirm) the rare variation. Because all samples used to ascertain (discover) SNPs or estimate their allele frequencies in specific population samples are of finite size, there will be some kind of ascertainment bias in every batch of data submitted to dbSNP.</p></blockquote></div><div id="Cnt_Ascertmnt_Bias.References"><h2 id="_Cnt_Ascertmnt_Bias_References_">References</h2><dl class="temp-labeled-list"><dt>1.</dt><dd><p class="no_top_margin">Marth GT, Czabarka E, Murvai J, Sherry ST. (2004) The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics. Jan;166(1):351-372</p></dd></dl></div><div id="bk_toc_contnr"></div></div></div>
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<div class="post-content"><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div><div class="small"><span class="label">Bookshelf ID: NBK573474</span></div><div style="margin-top:2em" class="bk_noprnt"><a class="bk_cntns" href="/books/n/helpsnpfaq/">Contents</a><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpsnpfaq/Cnt_Associat_Studies/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpsnpfaq/Cnt_Auto_SNP_Collect/" title="Next page in this title">Next ></a></div></div></div></div>
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