The value used for x was always 1, and the value used for y was the one-tailed 95% confidence limit. LR calculations for the kappa method used Eq. (6) from Brenner [39]: LRκ = n/(1 − κ), where κ represents the proportion of haplotypes in the population sample that are singletons (haplotypes observed only once), and n represents

the size of the population sample. A variety of data processing metrics were previously detailed for a subset of the low template blood serum samples used for this study [29]. As described in Section 2.2, samples that exhibited a single PCR failure during the initial, automated processing were manually reamplified to obtain PCR product that could be carried through to sequencing, whereas samples OSI-744 solubility dmso for which more than one of the eight target mtGenome regions failed to amplify were typically abandoned and not processed beyond amplification. Out of a total of 625 samples that were attempted, 37 were dropped due to PCR failure selleck chemical in two or more of the eight mtGenome target regions. As we previously reported, among the first 242 quantified samples processed, all 12 samples dropped due to multiple PCR failures had PCR DNA input quantities less than 10 pg/μl [29]. But, as PCR failures can occur due to primer binding site mutations, and those mutations may be haplogroup or lineage-specific, we explored the extent of PCR failure across all 588 completed haplotypes in relation

to the PCR strategy employed. An examination of the incidence and pattern of PCR failure among samples with primer binding region mutations indicates that such mutations are unlikely to have biased the final datasets for any of the GBA3 three population samples. A total of 52 polymorphisms, representing 34 distinct mutations, were found across the 16 primer binding regions. Primer binding region mutations were found in 46 of the 588 completed samples (7.8%), and overall had the potential to impact primer binding in 1.1% of the initial eight high-throughput PCR reactions performed per sample (a

total of 4704 PCR reactions). Yet, manual reamplification (due to near or complete PCR failure) was required in only eight of the 52 instances in which a mutation was later found in a PCR primer binding region; and thus primer binding region polymorphisms potentially caused PCR failure in just 1.4% of samples and 0.2% of amplifications. Further, as Fig. S1 demonstrates, the position of the mutation relative to the 3′ end of the primer was highly variable in these eight instances of reamplification, and thus the mutation may not have been the reason for the PCR failure in all eight cases. Among the 46 samples which were carried through to sequencing and later found to have polymorphisms in primer binding regions, five (8.9%) exhibited a mutation in more than one of the 16 primer binding regions, yet only three PCR failures (of 10 potentially affected reactions) were observed among these five samples.