Evaluating the Evidence for Transmission Distortion in Human Pedigrees

Meyer, Wynn K.; Arbeithuber, Barbara; Ober, Carole; Ebner, Thomas; Tiemann‐Boege, Irene; Hudson, Richard R.; Przeworski, Molly

doi:10.1534/genetics.112.139576

Cited by 45 publications

(66 citation statements)

References 76 publications

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“…It is important to mention that we have assumed the absence of genotyping errors when evaluating the performance of this BF approach. As previously demonstrated by Meyer et al (2012), transmission disequilibrium tests aimed to detect TRD are very sensitive to genotyping errors, a feature that can increase the rate of false positives. However, in the case of the half-sib design this problem is minimized because genotyping errors in the offspring generation have a low impact on TRD estimates due to the moderate-to-low contribution of each offspring in relation to remaining siblings.…”

Section: Resultsmentioning

confidence: 96%

A Flexible Bayesian Model for Testing for Transmission Ratio Distortion

et al. 2014

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Current statistical approaches to investigate the nature and magnitude of transmission ratio distortion (TRD) are scarce and restricted to the most common experimental designs such as F 2 populations and backcrosses. In this article, we describe a new Bayesian approach to check TRD within a given biallelic genetic marker in a diploid species, providing a highly flexible framework that can accommodate any kind of population structure. This model relies on the genotype of each offspring and thus integrates all available information from either the parents' genotypes or population-specific allele frequencies and yields TRD estimates that can be corroborated by the calculation of a Bayes factor (BF). This approach has been evaluated on simulated data sets with appealing statistical performance. As a proof of concept, we have also tested TRD in a porcine population with five half-sib families and 352 offspring. All boars and piglets were genotyped with the Porcine SNP60 BeadChip, whereas genotypes from the sows were not available. The SNP-by-SNP screening of the pig genome revealed 84 SNPs with decisive evidences of TRD (BF . 100) after accounting for multiple testing. Many of these regions contained genes related to biological processes (e.g., nucleosome assembly and co-organization, DNA conformation and packaging, and DNA complex assembly) that are critically associated with embryonic viability. The implementation of this method, which overcomes many of the limitations of previous approaches, should contribute to fostering research on TRD in both model and nonmodel organisms.

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Section: Resultsmentioning

confidence: 96%

A Flexible Bayesian Model for Testing for Transmission Ratio Distortion

et al. 2014

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“…Human samples were collected from anonymous donors by informed consent approved by the ethics commission of Upper Austria (Approval: F1-11). Sperm DNA was prepared as described previously (42) and was measured for quality and quantity with a spectrophotometer. In brief, DNA was extracted from ∼10 6 sperm cells (or 35 mg testis biopsy), using the Gentra Puregene Cell Kit (Qiagen), with the addition of 24 μM DTT (Sigma-Aldrich) and 60 μg/mL proteinase K (Qiagen) during the cell lysis step, followed by an overnight incubation at 37°C; 1 μL glycogen solution (Qiagen) was added during DNA precipitation.…”

Section: Methodsmentioning

confidence: 99%

Crossovers are associated with mutation and biased gene conversion at recombination hotspots

Arbeithuber

Betancourt²,

Ebner

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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225

218

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Meiosis is a potentially important source of germline mutations, as sites of meiotic recombination experience recurrent double-strand breaks (DSBs). However, evidence for a local mutagenic effect of recombination from population sequence data has been equivocal, likely because mutation is only one of several forces shaping sequence variation. By sequencing large numbers of single crossover molecules obtained from human sperm for two recombination hotspots, we find direct evidence that recombination is mutagenic: Crossovers carry more de novo mutations than nonrecombinant DNA molecules analyzed for the same donors and hotspots. The observed mutations were primarily CG to TA transitions, with a higher frequency of transitions at CpG than non-CpGs sites. This enrichment of mutations at CpG sites at hotspots could predominate in methylated regions involving frequent single-stranded DNA processing as part of DSB repair. In addition, our data set provides evidence that GC alleles are preferentially transmitted during crossing over, opposing mutation, and shows that GC-biased gene conversion (gBGC) predominates over mutation in the sequence evolution of hotspots. These findings are consistent with the idea that gBGC could be an adaptation to counteract the mutational load of recombination. meiotic recombination | crossover | sequence evolution | biased gene conversion | mutation M eiotic recombination, localized in recombination hotspots, not only increases genetic diversity via the formation of new haplotypes but is also an important driver of sequence evolution. The binding sites used by the human recombination machinery involving PRDM9 (PR domain containing 9) are more eroded in humans than the same sequences in chimps, given that PRDM9 in chimps uses different binding sites (1). Moreover, regions in close vicinity to these PRDM9 binding sites also showed a significant enrichment of polymorphisms in humans (2). In addition, within-and between-species sequence diversity positively correlates with regions of high recombination activity in humans (3-7) and other eukaryotes (reviewed in refs. 8-10).One process recognized as a major evolutionary force reshaping the genomic nucleotide landscape at recombination hotspots, as shown in humans (6), chimpanzees (6, 11), mice (12), yeast (13), and metazoans (14), is GC-biased gene conversion (gBGC). In gBGC, the repair of heteroduplex tracts formed during meiotic recombination leads to the nonMendelian segregation of alleles favoring GC over AT variants. The precise molecular mechanisms leading to gBGC have yet to be unraveled, but experimental evidence has shown that in crossovers (COs) of fission yeast, GC alleles can be overtransmitted within ∼1-2 kb in length of the double-strand break (DSB) region (13), implicating mismatch repair (15).However, it is also plausible that the higher sequence variation observed at recombination hotspots is a result of a mutagenic effect of recombination: meiotic recombination is initiated by DSBs, which are associated with an increased mutati...

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“…Human sperm and blood samples from anonymous donors were collected by informed consent approved by the ethics commission of Upper Austria (Approval: F1-11) at the IVF Landes-Frauen- und Kinderklinik Linz, Austria. Blood DNA was extracted using the PAXgene blood DNA kit (Qiagen), sperm DNA was extracted with the Gentra Puregene Cell Kit, as described previously 40 , 41 . In short, we extracted sperm DNA following instructions of the manufacturer except for the proteinase K digest which was performed overnight at 37 °C.…”

Section: Methodsmentioning

confidence: 99%

Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications

Arbeithuber

Makova

Tiemann‐Boege

2016

DNA Res

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The need in cancer research or evolutionary biology to detect rare mutations or variants present at very low frequencies (<10−5) poses an increasing demand on lowering the detection limits of available methods. Here we demonstrated that amplifiable DNA lesions introduce important error sources in ultrasensitive technologies such as single molecule PCR (smPCR) applications (e.g. droplet-digital PCR), or next-generation sequencing (NGS) based methods. Using templates with known amplifiable lesions (8-oxoguanine, deaminated 5-methylcytosine, uracil, and DNA heteroduplexes), we assessed with smPCR and duplex sequencing that templates with these lesions were amplified very efficiently by proofreading polymerases (except uracil), leading to G->T, and to a lesser extent, to unreported G->C substitutions at 8-oxoguanine lesions, and C->T transitions in amplified uracil containing templates. Long heat incubations common in many DNA extraction protocols significantly increased the number of G->T substitutions. Moreover, in ∼50-80% smPCR reactions we observed the random amplification preference of only one of both DNA strands explaining the known ‘PCR jackpot effect’, with the result that a lesion became indistinguishable from a true mutation or variant. Finally, we showed that artifactual mutations derived from uracil and 8-oxoguanine could be significantly reduced by DNA repair enzymes.

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Evaluating the Evidence for Transmission Distortion in Human Pedigrees

Cited by 45 publications

References 76 publications

A Flexible Bayesian Model for Testing for Transmission Ratio Distortion

A Flexible Bayesian Model for Testing for Transmission Ratio Distortion

Crossovers are associated with mutation and biased gene conversion at recombination hotspots

Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications

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