Population-specific variation in haplotype composition and heterozygosity at the POLB locus

Yamtich, Jennifer; Speed, William C.; Straka, Eva; Kidd, Judith R.; Sweasy, Joann B.; Kídd, Kenneth K.

doi:10.1016/j.dnarep.2008.12.005

Cited by 19 publications

(23 citation statements)

References 16 publications

(24 reference statements)

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“…These results indicate that identified variants are likely tumor-specific. None of the coding region mutations identified in this study are known to be germ line single nucleotide polymorphisms and are therefore likely somatic mutations that are associated with the tumor (43). Polymorphisms present in the UTR regions were also not observed in our samples (dbSNP, www.ncbi.nlm.nih.gov).…”

Section: Forty Percent Of Human Colorectal Tumors Harbor Mutations Inmentioning

confidence: 84%

Human POLB Gene Is Mutated in High Percentage of Colorectal Tumors

Donigan

Sun

Nemec

et al. 2012

Journal of Biological Chemistry

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Background:Previous small scale studies indicate that DNA polymerase ␤ variants are present in 30% of human tumors. Results: 40% of samples in a large human colorectal tumor collection harbor coding region variants, many of which exhibit altered function. Conclusion: Aberrant activity or fidelity phenotypes exhibited by variants may contribute to tumorigenesis. Significance: Expression of variants in human tumors plays a role in driving carcinogenesis.

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Section: Forty Percent Of Human Colorectal Tumors Harbor Mutations Inmentioning

confidence: 84%

Human POLB Gene Is Mutated in High Percentage of Colorectal Tumors

Donigan

Sun

Nemec

et al. 2012

Journal of Biological Chemistry

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“…Our typing methods are described in detail elsewhere. [5][6][7][8][9][10][11] As noted in those studies, an occasional typing failure persists after two attempts to obtain an acceptable result. Experience has shown that the yield from additional attempts at typing is extremely low.…”

Section: Methodsmentioning

confidence: 93%

Mini-haplotypes as lineage informative SNPs and ancestry inference SNPs

Pakstis

Fang²,

Furtado³

et al. 2012

Eur J Hum Genet

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We propose that haplotyped loci with high heterozygosity can be useful in human identification, especially within families, if recombination is very low among the sites. Three or more SNPs extending over small molecular intervals (o10 KB) can be identified in the human genome to define miniature haplotypes with moderate levels of linkage disequilibrium. Properly selected, these mini-haplotypes (or minihaps) consist of multiple haplotype lineages (alleles) that have evolved from the ancestral human haplotype but show no evidence of recurring recombination, allowing each distinct haplotype to be equated with an allele, all copies of which are essentially identical by descent. Historic recombinants, representing rare events that have drifted to common frequencies over many generations, can be identified in some cases, they do not equate to frequently recurring recombination. We have identified examples in our data collected on various projects and present eight such minihaplotypes comprised of informative SNPs. We also discuss the ideal characteristics and advantages of minihaps for human familial identification and ancestry inference, and compare them to other types of forensic markers in use and/or that have been proposed. We expect that it is possible to carry out a systematic search and identify a useful panel of mini-haplotypes, with even better properties than the examples presented here. Keywords: individual identification; SNP; haplotypes; minihaps; populations; ancestry inference INTRODUCTION Small molecular regions (for example, spanning o10 KB) comprised of three or more SNPs that define multi-allelic haplotype loci (minihaps) have the potential to convey more identity and ancestry-related information than a like number of single SNPs would convey. We defined and have advocated developing such multi-SNP haplotype systems as one type of forensic DNA marker, lineage informative SNPs, LISNPs (Pakstis et al, 1 Butler et al; 2 see also Ge et al 3 ). The multiple alleles (haplotypes) available in these more complex systems can serve to identify relatives with higher probabilities than simple di-allelic SNPs. By restricting the molecular extent to under B10 KB in regions with no recombination hot spot, recombination among the SNPs will be so rare that the possibility of recombination within a kindred approaches the mutation rate for SNPs. Depending on allele frequency variation among populations, minihaps could also be useful in ancestry inference. Direct comparison testing could also benefit from minihaps, but match probabilities will in general be population specific.Ge et al 3 described a strategy for identifying sets of SNPs with nearly complete to complete linkage disequilibrium (LD) among them. Although we agree that the objective of identifying haplotypes for forensic purposes is valid, we think their primary criterion of complete LD results in loci with lower than optimal heterozygosity. Based on our interest in haplotypes and their global patterns, we have recently begun pursuing the same objective of ...

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“…This resource is well documented among genetic studies and details can be found there. 22,[31][32][33] All subjects gave informed consent under protocols approved by the committees governing human subjects research relevant to each of the population samples. Sample descriptions and sample sizes can be found in the Allele Frequency Database by searching for the population names…”

Section: Methodsmentioning

confidence: 99%