Complex SNP-based haplotypes in three human helicases: implications for cancer association studies

Werner syndrome (WRN) gene variants and their association with altered function and age-associated diseases

Werner syndrome (WS) is a heritable autosomal recessive human disorder characterized by the premature onset of several age-associated pathologies including cancer. The protein defective in WS patients, WRN, is encoded by a member of the human RECQ gene family that contains both a DNA exonuclease and a helicase domain. WRN has been shown to participate in several DNA metabolic pathways including DNA replication, recombination and repair, as well as telomere maintenance and transcription modulation. Here we review base pair-level genetic variation that has been documented in WRN, with an emphasis on non-synonymous coding single nucleotide polymorphisms (SNPs) and their associations with anthropomorphic features, longevity and disease risk. These associations have been challenging to identify, as many reported WRN SNP associations appear to be further conditioned upon ethnic, age, gender or other environmental co-variables. The WRN variant phenotypic associations identified to date are intriguing, and several are of clear clinical import. Consequently, it will be important to extend these initial associations and to identify the mechanisms and conditions under which specific WRN variants may compromise WRN function to drive cellular and organismal phenotypes as well as disease risk.

WHY MATHEMATICS IS NEEDED TO UNDERSTAND COMPLEX GENETICS DISEASES

We discuss mathematical approaches to population genetics and evolutionary theory in the context of complex genetic disease. Mechanisms, which we discuss, include gene-environment interaction in lung cancer as well as classical mechanisms of stabilization of genetic disease such as overdominance, antagonistic pleiotropy and recurring mutations. Specific modeling approaches discussed include: (1) Mathematical model of the evolution of disease chromosome applied to mapping of a disease gene. (2) Iterated Galton–Watson branching process applied to modeling of trinucleotide expansion in triplet-repeat diseases. (3) Application of Ewens' sampling formula to analysis of Single Nucleotide Polymorphism haplotypes at disease-related genes. The aim of this paper is not to present an exhaustive review, but rather to advocate mathematical modeling approaches in a field of current interest.

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey

BACKGROUND

The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference genome, we set-up an analysis pipeline based on a short read de novo sequence assembler and a program designed to identify variation within short reads. To illustrate the potential of this technique, we present the results obtained with a randomly sheared, enzymatically generated, 2-3 kbp genome fraction of six pooled Meleagris gallopavo (turkey) individuals.

RESULTS

A total of 100 million 36 bp reads were generated, representing approximately 5-6% (approximately 62 Mbp) of the turkey genome, with an estimated sequence depth of 58. Reads consisting of bases called with less than 1% error probability were selected and assembled into contigs. Subsequently, high throughput discovery of nucleotide variation was performed using sequences with more than 90% reliability by using the assembled contigs that were 50 bp or longer as the reference sequence. We identified more than 7,500 SNPs with a high probability of representing true nucleotide variation in turkeys. Increasing the reference genome by adding publicly available turkey BAC-end sequences increased the number of SNPs to over 11,000. A comparison with the sequenced chicken genome indicated that the assembled turkey contigs were distributed uniformly across the turkey genome. Genotyping of a representative sample of 340 SNPs resulted in a SNP conversion rate of 95%. The correlation of the minor allele count (MAC) and observed minor allele frequency (MAF) for the validated SNPs was 0.69.

CONCLUSION

We provide an efficient and cost-effective approach for the identification of thousands of high quality SNPs in species currently lacking a sequenced genome and applied this to turkey. The methodology addresses a random fraction of the genome, resulting in an even distribution of SNPs across the targeted genome.

Mining for single nucleotide polymorphisms in pig genome sequence data

Background

Single nucleotide polymorphisms (SNPs) are ideal genetic markers due to their high abundance and the highly automated way in which SNPs are detected and SNP assays are performed. The number of SNPs identified in the pig thus far is still limited.

Results

A total of 4.8 million whole genome shotgun sequences obtained from the NCBI trace-repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project" were analysed for the presence of SNPs. Available BAC and BAC-end sequences and their naming and mapping information, all obtained from SangerInstitute FTP site, served as a rough assembly of a reference genome. In 1.2 Gb of pig genome sequence, we identified 98,151 SNPs in which one of the sequences in the alignment represented the polymorphism and 6,374 SNPs in which two sequences represent an identical polymorphism. To benchmark the SNP identification method, 163 SNPs, in which the polymorphism was represented twice in the sequence alignment, were selected and tested on a panel of three purebred boar lines and wild boar. Of these 163 in silico identified SNPs, 134 were shown to be polymorphic in our animal panel.

Conclusion

This SNP identification method, which mines for SNPs in publicly available porcine shotgun sequences repositories, provides thousands of high quality SNPs. Benchmarking in an animal panel showed that more than 80% of the predicted SNPs represented true genetic variation.

The Werner's syndrome 4330T>C (Cys1367Arg) gene variant does not affect the in vitro cytotoxicity of topoisomerase inhibitors and platinum compounds

PURPOSE

Werner's syndrome (WS) is a recessive disorder of premature onset of processes associated with aging. Defective DNA repair has been reported after exposure of cells isolated from WS patients to DNA-damaging agents. The germline 4330T>C (Cys1367Arg) variant in the WS gene (WRN) has been associated with protection from age-related diseases, suggesting it has a functional role. We studied whether the 4330T>C variant confers altered drug sensitivity in vitro.

METHODS

4330T>C was genotyped in 372 human lymphoblastoid cell lines (LCLs) from unrelated healthy Caucasian individuals using a TaqMan-based method. The study was powered to detect the effect of the 4330T>C genotypes after exposure to camptothecin (based upon preliminary data). The effect of the 4330T>C variant on the cytotoxicity of etoposide, carboplatin, cisplatin and daunorubicin was also tested. WRN expression in 57 LCLs was measured by microarray.

RESULTS

No significant difference between the IC50 of the cells was observed among genotypes (P = 0.46) after exposure to camptothecin. No association was also observed for etoposide, carboplatin, cisplatin, and daunorubicin (ANOVA, P > 0.05). WRN expression also did not vary across genotypes (ANOVA, P = 0.37).

CONCLUSION

These results suggest that this nonsynonymous variant has relatively normal function at the cellular level.

Environmental genotoxicants/carcinogens and childhood cancer: Bridgeable gaps in scientific knowledge

Cancer in children is a major concern in many countries. An important question is whether these childhood cancers are caused by something, or are just tragic random events. Causation of at least some children's cancers is suggested by direct and indirect evidence, including epidemiological data, and animal studies that predict early life sensitivity of humans to carcinogenic effects. Candidate risk factors include genotoxic agents (chemicals and radiation), but also diet/nutrition, and infectious agents/immune responses. With regard to likelihood of risks posed by genotoxicants, there are pros and cons. The biological properties of fetuses and infants are consistent with sensitivity to preneoplastic genotoxic damage. Recent studies of genetic polymorphisms in carcinogen-metabolizing enzymes confirm a role for chemicals. On the other hand, in numerous epidemiological studies, associations between childhood cancers and exposure to genotoxicants, including tobacco smoke, have been weak and hard to reproduce. Possibly, sensitive genetic or ontogenetic subpopulations, and/or co-exposure situations need to be discovered to allow identification of susceptible individuals and their risk factors. Among the critical knowledge gaps needing to be bridged to aid in this effort include detailed tissue and cellular ontogeny of carcinogen metabolism and DNA repair enzymes, and associations of polymorphisms in DNA repair enzymes with childhood cancers. Perinatal bioassays in animals of specific environmental candidates, for example, benzene, could help guide epidemiology. Genetically engineered animal models could be useful for identification of chemical effects on specific genes. Investigations of interactions between factors may be key to understanding risk. Finally, fathers and newborn infants should receive more attention as especially sensitive targets.

Single nucleotide polymorphisms: aging and diseases

Differences of more than 3 million nucleotides can bee seen comparing the genomes of two individuals as a result of single nucleotide polymorphism (SNP). More and more SNPs can be identified and it seems that these alterations are behind of several biological phenomena. Personal differences in these nucleotides result for example in elevated disease susceptibilities, that is, certain nucleotides are more frequent in patients suffering from different diseases comparing to the healthy population. SNPs may cause substantial alterations in the cells, e.g. the enzyme activity of the respective gene changes, but in other cases the effects of the SNPs are not so pronounced. Later results indicate that SNPs can be rendered to individuals living a longer life than the average. Perhaps these results will not directly lead to the lengthening of the maximal life span; however, genes that play an important role in the aging process could be identified. In this respect SNPs are important factors in determining the information level of the cells of individuals which determines the maximal life span (I. Semsei On the nature of aging. Mech. Ageing Dev . 2000; 117: 93-108), in turn SNP is one of the factors that determine the aging process. Since there are certain age-related diseases, the discovery and the description of the SNPs as a function of age and diseases may result in a better understanding of the common roots of aging and those diseases.

Substantial linkage disequilibrium across the dihydrolipoyl succinyltransferase gene region without Alzheimer's disease association

Association of the candidate gene DLST with late-onset Alzheimer's disease (LOAD) risk has been suggested on the basis of case-control studies. This gene, located on chromosome 14q24.3, encodes a subunit of a mitochondrial component known to be defective in AD, the alpha-ketoglutarate dehydrogenase complex. Positive reports have correlated different DLST alleles with LOAD, whereas other groups have failed to find any significant association. We therefore reexamined the association of DLST and LOAD in a more ethnically homogeneous series using three additional single nucleotide polymorphisms (SNP) located within or closely flanking either end of the DLST gene. Pairwise analysis of these SNPs indicated there was strong linkage disequilibrium across the DLST locus. Analysis of complex genotypes or haplotypes based upon all five SNP loci failed to identify a LOAD risk allele, suggesting that further studies of DLST in relation to AD are not warranted.

New Explicit Expressions for Relative Frequencies of Single-Nucleotide Polymorphisms With Application to Statistical Inference on Population Growth

We present new methodology for calculating sampling distributions of single-nucleotide polymorphism (SNP) frequencies in populations with time-varying size. Our approach is based on deriving analytical expressions for frequencies of SNPs. Analytical expressions allow for computations that are faster and more accurate than Monte Carlo simulations. In contrast to other articles showing analytical formulas for frequencies of SNPs, we derive expressions that contain coefficients that do not explode when the genealogy size increases. We also provide analytical formulas to describe the way in which the ascertainment procedure modifies SNP distributions. Using our methods, we study the power to test the hypothesis of exponential population expansion vs. the hypothesis of evolution with constant population size. We also analyze some of the available SNP data and we compare our results of demographic parameters estimation to those obtained in previous studies in population genetics. The analyzed data seem consistent with the hypothesis of past population growth of modern humans. The analysis of the data also shows a very strong sensitivity of estimated demographic parameters to changes of the model of the ascertainment procedure.

A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data

Discovery of non-synonymous single nucleotide polymorphisms (nsSNP), which cause amino acid substitutions, is important because they are more likely to alter protein function than synonymous SNPs (sSNP) or those SNPs that do not result in amino acid changes. By changing the coding sequences, nsSNP may play a role in heritable differences between individual organisms. In the chicken and many other vertebrates, the main obstacle for identifying nsSNP is that there is insufficient protein and mRNA sequence information for self-species referencing and thus, determination of the correct reading frame for expressed sequence tags (ESTs) is difficult. Therefore, in order to estimate the correct reading frame at nsSNP in chicken ESTs, a double-screening approach was designed using self- or cross-species protein referencing, in addition to the ESTScan coding region estimation programme. Starting with 23 427 chicken ESTs, 1210 potential SNPs were discovered using a phred/phrap/polyphred/consed pipeline process and among these, 108 candidate nsSNP were identified with the double screening method. A searchable SNP database (chicksnps) for the candidate chicken SNPs, including both nsSNPs and sSNPs is available at http://chicksnps.afs.udel.edu. The chicken SNP data described in this paper have been submitted to the data base SNP under National Center for Biotechnology Information assay ID ss4387050-ss4388259.

Proposal for an allele nomenclature system based on the evolutionary divergence of haplotypes

The classical view of what constitutes an "allele" has been challenged by recent findings of a great deal of human genetic variability, i.e., we can expect, on average, one variant site every 100-250 bases of our haploid genome. The haplotype is defined as "the patterns of co-occurrence of variant sites on the same chromosome" (and therefore within each particular gene). Sufficient evidence exists for the divergence of haplotypes during evolution of Homo sapiens sapiens, and the total number of haplotypes per gene will reflect the amount of time any particular ethnic group has existed on the planet, e.g., greatest in Africans, fewer in East Asians, and still fewer in Caucasians. If the average gene spans 30 kb, we can expect approximately 170 polymorphic variant sites per gene in the world population. We do not see 2(170) haplotypes, however; we might find only 10 to 200 haplotypes (depending on the gene's size and degree of conservation of the gene product). This finite number allows for a reasonable haplotype nomenclature system for each gene, based on evolutionary divergence. For polymorphic variants (i.e., frequency > or = 0.01), I propose using Arabic numerals for the major clades (e.g., *1, *2, em leader *20, *21), capital letters for sublineages (e.g., *2A, *2B, *2C), and Arabic numerals for sub-sublineages (e.g., *22G12, *22G13); additional subcategories may be added, in an alternating number/letter/number/letter sequence, depending on the complexity of present-day haplotypes of a particular gene. Web sites with a web master and external advisory committee should be set up for each gene superfamily, family, or individual gene (depending on complexity), and an international haplotype nomenclature committee, perhaps comprised of several dozen of these web masters, should oversee haplotype nomenclature for the entire human genome. The higher heterozygosity and multiallelic nature makes haplotypes more informative than biallelic SNPs. Ultimately, our knowledge of haplotype patterns, rather than single variant sites, of perhaps several hundred genes will likely be helpful in finding associations between genotype and any multiplex phenotype (e.g., complex diseases including cancer, and/or toxicity of pharmaceutical agents or environmental pollutants).

Polymorphisms in the human AH receptor

The AH receptor (AHR) mediates toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) as well as induction of three cytochrome P450 enzymes and certain Phase II enzymes. In laboratory animals, genetic variations in the AHR lead to substantial differences in sensitivity to biochemical and toxic effects of TCDD and related compounds. Relatively few polymorphisms have been discovered in the human AHR gene; these occur predominantly in exon 10, a region that encodes a major portion of the transactivation domain of the receptor that is responsible for regulating expression of other genes. In human populations there is a wide range of variation in responses regulated by the AHR for example, induction of CYP1A1. Some variation in human responsiveness likely is due to genetically based variations in AHR structure. Thus far, however, only one pair of polymorphisms, those at codons 517 and 570, has been shown to have a clear cut and strong effect on the phenotype of an AHR-mediated response. The search continues for polymorphisms that alter AHR function because this receptor is a central factor in determining responses to important environmental contaminants and also plays a physiologic role in early development in mammals.