Distributions of IBD_half by degree of cousinship, assessed with simulated pedigrees for Ashkenazim and Europeans.

<p>Plotted, for each combination of IBD_half and number of IBD segments, are the 95th percentile, 50th percentile and 5th percentile degrees of cousinship based on 1 million simulated pedigrees. A–C) Ashkenazi pairs, D–F) European pairs, G–I) The differences between Ashkenazi and European results, presented in the prior panels, are represented in grey. Darker grey indicates higher number of differences. Each <i>n</i>th cousinship category was scaled by the expected number of <i>n</i>th degree cousins given a model of population growth (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#pone-0034267-t002" target="_blank">Table 2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#s4" target="_blank"><i>Methods</i></a>). Simulations were conducted by specifying an extended pedigree and creating simulated genomes for the pedigree by mating individuals drawn from a pool of empirical genomes. Pairs of individuals who appear to share IBD_half that was not inherited through the specified simulated pedigree are marked in grey in the A–F panels.</p

IBD statistics for a subset of HGDP-CEPH and 23andMe population samples^a.

a<p>See also Supporting Information, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#pone.0034267.s003" target="_blank">Table S1</a>, for IBD statistics in all 121 populations.</p>b<p>“IBD_half” is defined as the sum of the lengths of genomic segments where two individuals are inferred to share DNA identical by state for at least one of the homologous chromosomes.</p>c<p>“F_IBD” is defined as the fraction of pairs that share at least one IBD_half segment greater than or equal to 7 cM.</p

Fraction of 23andMe individuals with detectable distant relatives within subsamples inferred using IBD_half.

<p>A) The fraction of individuals with at least one predicted relative (2^nd–9^th cousin) given datasets of varying size. All datasets were drawn from a dataset of 5000 individuals with European ancestry. All closely related individuals (i.e., 1^st or 2^nd generation family) were removed before performing the analysis. B) The number of predicted cousins of each degree of cousinship given the dataset size. Predictions based on parameters obtained from simulations (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#pone-0034267-g004" target="_blank">Figure 4e</a>).</p

Relationship between degree of cousinship and IBD_half metrics.

<p>We used pedigree-based simulations to characterize the relationship between IBD_half metrics and degrees of cousinship for multiple population samples. a) Genomic data from a European sample were used to simulate an 11-generation pedigree. The joint distribution of IBD_half and number of IBD_half segments is shown for each pairwise comparison from the pedigree simulations. GP/GC indicates grandparent/grandchild pairs. b) For each of eight populations, we summarize the distribution of IBD_half by plotting IBD_half(n) for the population by degree of cousinship. The degrees of cousinship distinguished by IBD_half(n) asymptotes at different levels of IBD in ethnolinguistically-defined populations. Simulations were run on phased samples from several HGDP-CEPH population samples and European, Asian and Ashkenazi samples from a 23andMe customer dataset. Simulations were conducted by specifying an extended pedigree structure and simulating genomes for the pedigree by mating individuals drawn from a pool of empirical genomes (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#s4" target="_blank"><i>Methods</i></a>).</p

Expected extent of IBD and number of cousins for 1st–10th degrees of cousinship.

a<p>Theoretical expectation of the amount of IBD across the genome shared between <i>n</i>th cousins, assuming 3600 cM across the entire genome. It should be emphasized this description assumes a single common ancestor for a pair of cousins; multiple shared common ancestors will increase the predicted IBD sharing.</p>b<p>The fraction of <i>n</i>th degree cousins detected using our IBD algorithm and based on simulated pedigrees of up to 10th degree cousins (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#s4" target="_blank"><i>Methods</i></a>).</p>c<p>Assuming a specific model of pedigree and population growth over the past 11 generations (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#s4" target="_blank"><i>Methods</i></a>).</p>d<p>The expected number of cousins detectable with our IBD algorithm (N^dc) was calculated by multiplying the probability of detecting an <i>n</i>th cousin by the number of <i>n</i>th cousins obtained from our pedigree model of population growth (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#s4" target="_blank"><i>Methods</i></a>).</p>e<p>Given the variation in population growth at >9 generations ago, combined with a low power of detection for 9th or 10th cousins, we have indicated the number of detectable cousins for those categories as not applicable, “NA”.</p

Distributions of IBD_half for pairs of individuals within three human populations.

<p>The average amount of DNA that is identical by descent (mean IBD_half) varies widely across HGDP-CEPH, European, Asian and Ashkenazi populations. We present distributions of pairwise comparisons with IBD_half segments ≥7 cM for the (a) Karitiana Native Americans, (b) Yakut of Siberia, (c) Ashkenazi Jews primarily from the United States. Prior to the analysis, individuals were eliminated in order to remove close relationships (sibling, parent-child, avuncular, grandparent-grandchild, and 1st cousin pairs) (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#s4" target="_blank"><i>Methods</i></a>). Pairs with less than 7 cM IBD_half are not displayed. Distributions of IBD_half for additional HGDP-CEPH samples are presented in Supplementary Material (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034267#pone.0034267.s001" target="_blank">Figure S1</a>).</p

High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number

Digital PCR enables the absolute quantitation of nucleic acids in a sample. The lack of scalable and practical technologies for digital PCR implementation has hampered the widespread adoption of this inherently powerful technique. Here we describe a high-throughput droplet digital PCR (ddPCR) system that enables processing of ∼2 million PCR reactions using conventional TaqMan assays with a 96-well plate workflow. Three applications demonstrate that the massive partitioning afforded by our ddPCR system provides orders of magnitude more precision and sensitivity than real-time PCR. First, we show the accurate measurement of germline copy number variation. Second, for rare alleles, we show sensitive detection of mutant DNA in a 100 000-fold excess of wildtype background. Third, we demonstrate absolute quantitation of circulating fetal and maternal DNA from cell-free plasma. We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics