Genetic and functional heterogeneity of the hepatitis C virus p7 ion channel during natural chronic infection

The present study describes natural genetic heterogeneity of hepatitis C virus (HCV) p7 protein, the ion channel that plays a critical role in assembly and release of HCV, within 299 variants isolated from serum specimens of 27 chronically infected patients, 12 of whom with human immunodeficiency virus (HIV) co-infection. Liver fibrosis stage was inversely correlated with p7 synonymous substitutions (dS) (p = 0.033), and indices of p7 genetic diversity were significantly higher in HIV-negative subjects compared to HIV-positive subjects (dS, p = 0.005; non-synonymous substitutions (dN), p = 0.002; dN/dS ratio, p = 0.024; amino acid distances, p = 0.007). Six p7 genes with naturally occurring unique amino acid variations were selected for in vitro study. The variants demonstrated diversified functional heterogeneity in vitro, with one variant from a subject with severe liver disease displaying hyperactive ion channel function, as well as other variants presenting altered pH-activated channel gating activities.     

To what extent do scans of non-synonymous SNPs complement denser genome-wide association studies?

Several studies involving genome-wide scans of non-synonymous SNPs (nsSNPs) have successfully identified loci contributing to common complex diseases. We were interested in the extent to which these small scans involving a few thousand non-synonymous markers might complement the results from denser genome-wide association studies. We assessed the degree to which three commercially available genome-wide marker panels tagged nsSNPs on the Illumina HumanNS-12 BeadChip, a product specifically designed to capture non-synonymous variation. We demonstrate that commercially available genome-wide panels already tag the majority of common non-synonymous variants on the NS-12 BeadChip, indicating that with respect to capturing common non-synonymous variation, information from the NS-12 BeadChip is largely redundant. In contrast, genome-wide panels fail to capture most of the rare SNPs present on the NS-12 BeadChip. Power calculations reveal that non-synonymous scans involving sample sizes typical of the current wave of genome-wide association studies are unlikely to identify rare variants of small effect, but could conceivably identify rare variants of intermediate penetrance. We conclude that non-synonymous scans may facilitate the identification of rare variants of intermediate penetrance that would not otherwise be detectable using dense genome-wide panels, but are unlikely to uniquely identify common variants contributing to complex disease variation.     

An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy

PurposeSpinal muscular atrophy is a common autosomal-recessive disorder caused by mutations of the SMN1 gene. Spinal muscular atrophy carrier screening uses dosage-sensitive methods that determine SMN1 copy number, and the frequency of carriers varies by ethnicity, with detection rates ranging from 71 to 94% due to the inability to identify silent (2 + 0) carriers with two copies of SMN1 on one chromosome 5 and deletion on the other. We hypothesized that identification of deletion and/or duplication founder alleles might provide an approach to identify silent carriers in various ethnic groups.MethodsSMN1 founder alleles were investigated in the Ashkenazi Jewish population by microsatellite analysis and next-generation sequencing.ResultsAn extended haplotype block, specific to Ashkenazi Jewish SMN1 duplications, was identified by microsatellite analysis, and next-generation sequencing of SMN1 further defined a more localized haplotype. Of note, six novel SMN1 sequence variants were identified that were specific to duplications and not present on single-copy alleles. The haplotype was also identified on SMN1 duplication alleles in additional ethnic groups.ConclusionIdentification of these novel variants in an individual with two copies of SMN1 significantly improves the accuracy of residual risk estimates and has important implications for spinal muscular atrophy carrier screening.Genet Med16 2, 149–156.     

Cholesteryl ester transfer protein (CETP) I405V polymorphism and longevity in Italian centenarians

A common polymorphism (I405V) in exon 14 of the cholesteryl ester transfer protein (CETP) gene has been recently associated to healthy aging in Ashkenazi Jewish. In order to study this genetic effect in long-lived individuals with a different ethnicity, we analyzed the allele and genotype distributions of the CETP polymorphism a sample of Italian centenarians. Our result does not confirm the association between the I405V CETP variation and the healthy aging phenotype described in the Ashkenazi Jewish population and suggests that other gene environment interactions contribute to longevity.     

A genome-wide scan of 10?000 gene-centric variants and colorectal cancer risk

Genome scans based on gene-centric single nucleotide polymorphisms (SNPs) have been proposed as an efficient approach to identify disease-causing variants that is complementary to scans based on tagging SNPs. Adopting this approach to identify low-penetrance susceptibility alleles for colorectal cancer (CRC) we analysed genotype data from 9109 gene-centric SNPs, 7014 of which were non-synonymous (nsSNPs), in 2873 cases and 2871 controls using Illumina iselect arrays. Overall the distribution of associations was not significantly different from the null. No SNP achieved globally significant association after correction for multiple testing (lowest P value 1.7 × 10⁻⁴, rs727299). We then analysed the dataset incorporating information on the functional consequences of nsSNPs. We used results from the in silico algorithm PolyPhen as prior information to weight the association statistics, with weights estimated from the observed test statistics within predefined groups of SNPs. Incorporating this information did not, however, yield any further evidence of a specific association (lowest P value 2.2 × 10⁻⁴, rs1133950). There was a strong relationship between effect size and SNPs predicted to be damaging (P=1.63 × 10⁻⁵), however, these variants which are most likely to impact on risk are rare (MAF<5%). Hence although the rationale for searching for low-penetrance cancer susceptibly alleles by conducting genome-wide scans of coding changes is strong, in practice it is likely that natural selection has rendered such alleles to be too rare to be detected by association studies of the size employed.     

A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population

The detection of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) with precision from high-throughput data remains a significant bioinformatics challenge. Accurate detection is necessary before next-generation sequencing can routinely be used in the clinic. In research, scientific advances are inhibited by gaps in data, exemplified by the underrepresented discovery of rare variants, variants in non-coding regions and indels. The continued presence of false positives and false negatives prevents full automation and requires additional manual verification steps. Our methodology presents applications of both pattern recognition and sensitivity analysis to eliminate false positives and aid in the detection of SNP/indel loci and genotypes from high-throughput data. We chose FK506-binding protein 51(FKBP5) (6p21.31) for our clinical target because of its role in modulating pharmacological responses to physiological and synthetic glucocorticoids and because of the complexity of the genomic region. We detected genetic variation across a 160 kb region encompassing FKBP5. 613 SNPs and 57 indels, including a 3.3 kb deletion were discovered. We validated our method using three independent data sets and, with Sanger sequencing and Affymetrix and Illumina microarrays, achieved 99% concordance. Furthermore we were able to detect 267 novel rare variants and assess linkage disequilibrium. Our results showed both a sensitivity and specificity of 98%, indicating near perfect classification between true and false variants. The process is scalable and amenable to automation, with the downstream filters taking only 1.5 h to analyze 96 individuals simultaneously. We provide examples of how our level of precision uncovered the interactions of multiple loci, their predicted influences on mRNA stability, perturbations of the hsp90 binding site, and individual variation in FKBP5 expression. Finally we show how our discovery of rare variants may change current conceptions of evolution at this locus.     

Novel variants in human Aquaporin-4 reduce cellular water permeability

Cerebral edema contributes significantly to morbidity and mortality after brain injury and stroke. Aquaporin-4 (AQP4), a water channel expressed in astrocytes, plays a key role in brain water homeostasis. Genetic variants in other aquaporin family members have been associated with disease phenotypes. However, in human AQP4, only one non-synonymous single-nucleotide polymorphism (nsSNP) has been reported, with no characterization of protein function or disease phenotype. We analyzed DNA from an ethnically diverse cohort of 188 individuals to identify novel AQP4 variants. AQP4 variants were constructed by site-directed mutagenesis and expressed in cells. Water permeability assays in the cells were used to measure protein function. We identified 24 variants in AQP4 including four novel nsSNPs (I128T, D184E, I205L and M224T). We did not observe the previously documented M278T in our sample. The nsSNPs found were rare ( approximately 1-2% allele frequency) and heterozygous. Computational analysis predicted reduced function mutations. Protein expression and membrane localization were similar for reference AQP4 and the five AQP4 mutants. Cellular assays confirmed that four variant AQP4 channels reduced normalized water permeability to between 26 and 48% of the reference (P < 0.001), while the M278T mutation increased normalized water permeability (P < 0.001). We identified multiple novel AQP4 SNPs and showed that four nsSNPs reduced water permeability. The previously reported M278T mutation resulted in gain of function. Our experiments provide insight into the function of the AQP4 protein. These nsSNPs may have clinical implications for patients with cerebral edema and related disorders.     

Carrier screening in the era of expanding genetic technology

PurposeThe Center for Jewish Genetics provides genetic education and carrier screening to individuals of Jewish descent. Carrier screening has traditionally been performed by targeted mutation analysis for founder mutations with an enzyme assay for Tay–Sachs carrier detection. The development of next-generation sequencing (NGS) allows for higher detection rates regardless of ethnicity. Here, we explore differences in carrier detection rates between genotyping and NGS in a primarily Jewish population.MethodsPeripheral blood samples or saliva samples were obtained from 506 individuals. All samples were analyzed by sequencing, targeted genotyping, triplet-repeat detection, and copy-number analysis; the analyses were carried out at Counsyl.ResultsOf 506 individuals screened, 288 were identified as carriers of at least 1 condition and 8 couples were carriers for the same disorder. A total of 434 pathogenic variants were identified. Three hundred twelve variants would have been detected via genotyping alone. Although no additional mutations were detected by NGS in diseases routinely screened for in the Ashkenazi Jewish population, 26.5% of carrier results and 2 carrier couples would have been missed without NGS in the larger panel.ConclusionIn a primarily Jewish population, NGS reveals a larger number of pathogenic variants and provides individuals with valuable information for family planning.Genet Med 18 12, 1214–1217.     

Association analysis of the SHC1 gene locus with longevity in the Japanese population

The SHC1 gene encodes a signaling and transforming protein that has been implicated in the aging process in worms and mammals. In this study we examined 230 Japanese centenarians and 180 healthy younger controls and looked at the SHC1 locus as a candidate region that may be associated with longevity. We identified 12 single nucleotide polymorphisms (SNPs) within a 10-kb region encompassing the entire SHC1 gene from the DNA of 30 centenarians and 24 healthy younger controls. Five SNPs, including three nonsynonymous sites, lay within coding elements, six were located within introns, and one was in the 3 untranslated region. All of these SNPs were relatively rare, with a minor allele frequency of less than 5% in our subjects. A pairwise linkage disequilibrium analysis using the r ² statistic showed that two of the SNP pairs are in tight linkage disequilibrium at this locus. We investigated the possible association of SHC1 with longevity using association analyses with allelotypes and haplotypes but found that the SNPs identified in SHC1 had no impact on longevity for Japanese centenarians.Abbreviations LD Linkage disequilibrium - SNP Single nucleotide polymorphism     

Glucocerebrosidase mutations are not a common risk factor for Parkinson disease in North Africa

Mutations in the glucocerebrosidase gene (GBA) have recently been associated with an increased risk of Parkinson disease (PD). GBA mutations have been observed to be particularly prevalent in the Ashkenazi Jewish population. Interestingly, this population also has a high incidence of the Lrrk2 p.G2019S mutation which is similar in North African Arab-Berber populations. Herein, our sequencing of the GBA gene, in 33 North African Arab-Berber familial parkinsonism probands, identified two novel mutations in three individuals (p.K-26R and p.K186R). Segregation analysis of these two variants did not support a pathogenic role. Genotyping of p.K-26R, p.K186R and the common p.N370S in an ethnically matched series consisting of 395 patients with PD and 372 control subjects did not show a statistically significant association (P > 0.05). The p.N370S mutation was only identified in 1 sporadic patient with PD and 3 control subjects indicating that the frequency of this mutation in the North African Arab-Berber population is much lower than that observed in Ashkenazi Jews, and therefore arose in the latter after expansion of the Lrrk2 p.G2019S variant in North Africa.     

Gender differences in the IL6 -174G>C and ESR2 1730G>A polymorphisms and the risk of Parkinson's disease

The −174G>C (rs1800795) single nucleotide polymorphism (SNP) in the promoter of the interleukin-6 (IL6) gene and the 1730G>A (rs4986938) SNP in the estrogen receptor beta (ESR2) may influence the risk of Parkinson's disease (PD). We investigated these SNPs in 380 unrelated US Caucasian PD cases and 522 controls, including 452 individuals of Ashkenazi Jewish (AJ) origin (260 PD, 192 controls). The G allele of the −174G>C SNP was more common in AJ PD cases (p = 0.033) as well as in Non-Jewish (NJ) men with PD (p = 0.022). The GG genotype increased the risk of PD by over two fold in NJ men (OR = 2.11, 95%CI: 1.14-3.89, p = 0.017), and approached significance in the total AJ group with PD (OR = 1.42, 95%CI: 0.97-2.06, p = 0.067). The A allele of the ESR2 1730G>A SNP was associated with a decreased risk for PD in AJ women, and in this group, having the AA genotype decreased the risk of PD by half (OR = 0.45, 95%CI: 0.22-0.92, p = 0.029). Our data supports a role for the IL6 −174G>C G allele in AJ individuals overall. In NJ Caucasians, this role appears to be gender mediated. In both groups, the effect is independent from ESR2 1730G>A. A separate association for the ESR2 1730G>A SNP was found exclusively in women of AJ descent. Other polymorphisms in tight linkage disequilibrium with the SNP differentially influencing expression, ethnic differences in allele distribution, and gender differences in genetic load related to PD, may underlie our findings. Larger studies in diverse populations, including analysis of surrounding regions are recommended.     

Evaluation and identification of damaged single nucleotide polymorphisms in COL1A1 gene involved in osteoporosis

Introduction

Single-nucleotide polymorphisms (SNPs) are biomarkers for exploring the genetic basis of many complex human diseases. The prediction of SNPs is promising in modern genetic analysis but it is still a great challenge to identify the functional SNPs in a disease-related gene. The computational approach has overcome this challenge and an increase in the successful rate of genetic association studies and reduced cost of genotyping have been achieved. The objective of this study is to identify deleterious non-synonymous SNPs (nsSNPs) associated with the COL1A1 gene.

Material and methods

The SNPs were retrieved from the Single Nucleotide Polymorphism Database (dbSNP). Using I-Mutant, protein stability change was calculated. The potentially functional nsSNPs and their effect on proteins were predicted by PolyPhen and SIFT respectively. FASTSNP was used for estimation of risk score.

Results

Our analysis revealed 247 SNPs as non-synonymous, out of which 5 nsSNPs were found to be least stable by I-Mutant 2.0 with a DDG value of > –1.0. Four nsSNPs, namely rs17853657, rs17857117, rs57377812 and rs1059454, showed a highly deleterious tolerance index score of 0.00 with a change in their physicochemical properties by the SIFT server. Seven nsSNPs, namely rs1059454, rs8179178, rs17853657, rs17857117, rs72656340, rs72656344 and rs72656351, were found to be probably damaging with a PSIC score difference between 2.0 and 3.5 by the PolyPhen server. Three nsSNPs, namely rs1059454, rs17853657 and rs17857117, were found to be highly polymorphic with a risk score of 3-4 with a possible effect of non-conservative change and splicing regulation by FASTSNP.

Conclusions

Three nsSNPs, namely rs1059454, rs17853657 and rs17857117, are potential functional polymorphisms that are likely to have a functional impact on the COL1A1 gene.     

Effect of interleukin-6 polymorphisms on human longevity: a systematic review and meta-analysis

Several studies have assessed changes in frequency of −174 interleukin (IL)-6 single nucleotide polymorphism (SNP) with age. If IL-6 tracks with disability and age-related diseases, then there should be reduction, in the oldest old, of the frequency of homozgyous GG subjects, who produce higher IL-6 levels. However, discordant results have been obtained. To explore the relationship between this polymorphism and longevity, we analyzed individual data on long-living subjects and controls from eight case-control studies conducted in Europeans, using meta-analysis. There was no significant difference in the IL-6 genotype between the oldest old and controls (Odds Ratio [OR] = 0.96; 95% C.I.: 0.77-1.20; p = 0.71), but there was significant between-study heterogeneity (I² = 55.5%). In a subgroup analyses when male centenarians from the three Italian studies were included, the frequency of the IL-6 −174 GG genotype was significantly lower than the other genotypes (OR = 0.49; 95% C.I.: 0.31-0.80; p = 0.004), with no evidence of heterogeneity (I² = 0%). Our data supports a negative association between the GG genotype of IL-6 SNP and longevity in Italian centenarians, with males who carry the genotype being two times less likely to reach extreme old age compared with subjects carrying CC or CG genotypes. These findings were not replicated in other European groups suggesting a possible interaction between genetics, sex and environment in reaching longevity.     

The Mn-superoxide dismutase single nucleotide polymorphism rs4880 and the glutathione peroxidase 1 single nucleotide polymorphism rs1050450 are associated with aging and longevity in the oldest old

The free radical theory of aging states that reactive oxygen species (ROS) play a key role in age-related accumulation of cellular damage, and consequently influence aging and longevity. Therefore, variation in genes encoding proteins protecting against ROS could be expected to influence variation in aging and life span. The rs4880 and rs1050450 SNPs in the manganese superoxide dismutase (MnSOD) and glutathione peroxidase 1 (GPX1) genes, respectively, are associated with age-related diseases and appear to affect the activities of the encoded variant proteins.In this study we genotyped these SNPs in 1650 individuals from the Danish 1905 cohort (follow-up time: 1998-2008, age at intake: 92-93 years, number of deaths: 1589 (96.3%)) and investigated the association with aging and longevity. We found decreased mortality of individuals holding either the MnSOD rs4880 C or the GPX1 rs1050450 T alleles (HR (MnSOD(CC/CT)) = 0.91, P = 0, p = 0.002 and HR (GPX1(TT/TC)) = 0.93, p = 0.008). Furthermore, a synergetic effect of the alleles was observed (HR = 0.76, p = 0.001). Finally, moderate positive associations with good self rated health, decreased disability and increased cognitive capacity were observed. Our results thus indicate that genetic variation in MnSOD and GPX1 may be associated with aging and longevity.     

Bayesian approach to discovering pathogenic SNPs in conserved protein domains

The success rate of association studies can be improved by selecting better genetic markers for genotyping or by providing better leads for identifying pathogenic single nucleotide polymorphisms (SNPs) in the regions of linkage disequilibrium with positive disease associations. We have developed a novel algorithm to predict pathogenic single amino acid changes, either nonsynonymous SNPs (nsSNPs) or missense mutations, in conserved protein domains. Using a Bayesian framework, we found that the probability of a microbial missense mutation causing a significant change in phenotype depended on how much difference it made in several phylogenetic, biochemical, and structural features related to the single amino acid substitution. We tested our model on pathogenic allelic variants (missense mutations or nsSNPs) included in OMIM, and on the other nsSNPs in the same genes (from dbSNP) as the nonpathogenic variants. As a result, our model predicted pathogenic variants with a 10% false-positive rate. The high specificity of our prediction algorithm should make it valuable in genetic association studies aimed at identifying pathogenic SNPs.     

Study of carrier frequency of Warsaw breakage syndrome in the Ashkenazi Jewish population and presentation of two cases

Warsaw breakage syndrome (WABS), caused by bi‐allelic variants in the DDX11 gene, is a rare cohesinopathy characterized by pre‐ and postnatal growth retardation, microcephaly, intellectual disability, facial dysmorphia, and sensorineural hearing loss due to cochlear hypoplasia. The DDX11 gene codes for an iron–sulfur DNA helicase in the Superfamily 2 helicases and plays an important role in genomic stability and maintenance. Fourteen individuals with WABS have been previously reported in the medical literature. Affected individuals have been of various ethnic backgrounds with different pathogenic variants. We report two unrelated individuals of Ashkenazi Jewish descent affected with WABS, who are homozygous for the c.1763‐1G>C variant in the DDX11 gene. Their phenotype is consistent with previously reported individuals. RNA studies showed that this variant causes an alternative splice acceptor site leading to a frameshift in the open reading frame. Carrier screening of the c.1763‐1G>C variant in the Jewish population revealed a high carrier frequency of 1 in 68 in the Ashkenazi Jewish population. Due to the high carrier frequency and the low number of affected individuals, we hypothesize a high rate of miscarriage of homozygous fetuses and/or subfertility for carrier couples. If the carrier frequency is reproducible in additional Ashkenazi Jewish populations, we suggest including DDX11 to Ashkenazi Jewish carrier screening panels.     

Identification of sequence variants in the CCL3 chemokine gene family in the HapMap west african reference population

Gene copy number variation (CNV) of the CC Chemokine ligand 3-Like-1 (CCL3L1) gene located on chromosome 17q12 has been associated with many diseases, including viral infections and autoimmune diseases. High sequence homology between CCL3L1 and three other related genes within the same cluster, CCL3, CCL3L2, and CCL3L3, make it difficult to determine the copy number of each gene as well as distinguishing variants within each gene versus between genes. We identified a total of 50 SNPs, 31 known and 19 novel SNPs, in a subset of West Africa Reference (Yoruba individuals from Ibadan, Nigeria (YRI)) samples from HapMap. One of these previously unidentified variations is a non-synonymous change while several other unreported variations are located near potential regulatory sites. The variations identified in these immune-related genes from this study will shed light in the understanding of both structural and nucleotide polymorphisms that can be used in association studies of diseases in populations.     

Evaluation of resequencing on number of tag SNPs of 13 atherosclerosis-related genes in Thai population

In the candidate gene approach, information about the distribution of single nucleotide polymorphisms (SNPs) is a crucial requirement for choosing efficient markers necessary for a case-control association study. To obtain such information, we discovered SNPs in 13 genes related to atherosclerosis by resequencing exon-flanking regions of 32 healthy Thai individuals. In total, 194 polymorphisms were identified, 184 of them SNPs, four insertions, and the rest deletions. Fifty-nine of the SNPs were characterized as novel polymorphisms, and these accounted for 30% of the identified SNPs. Comparing allele frequency distributions of the Thai population with other Asian populations shows similar patterns. In contrast, a low correlation pattern (r = 0.521) was found when comparing with either Caucasian or African populations. However, some rare alleles (rs11574541 and rs10874913) are found in the Thai population but not in other Asian populations. Most of the novel SNPs found were located outside the haplotype blocks generated by known SNPs in the Thai population. Only 5.77% of the novel SNPs lies in these defined haplotype blocks. The selection of haplotype-tagging SNPs shows that 8 of 13 genes benefited from the ethnic-specific genotype information. That is, when at least one novel SNP was present, the tagging SNPs chosen were altered. Functional prediction of 16 nonsynonymous SNPs (nsSNPs) by three different algorithm tools demonstrated that five nsSNPs possibly alter their corresponding protein functions. These results provide necessary information for conducting further genetic association studies involving the Thai population and demonstrate that resequencing of candidate genes provides more complete information for full genetic studies. Chintana Tocharoentanaphol and Somying Promso contributed equally to this work.     

MtDNA evidence for a genetic bottleneck in the early history of the Ashkenazi Jewish population

The relative roles of natural selection and accentuated genetic drift as explanations for the high frequency of more than 20 Ashkenazi Jewish disease alleles remain controversial. To test for the effects of a maternal bottleneck on the Ashkenazi Jewish population, we performed an extensive analysis of mitochondrial DNA (mtDNA) hypervariable segment 1 (HVS-1) sequence and restriction site polymorphisms in 565 Ashkenazi Jews from different parts of Europe. These patterns of variation were compared with those of five Near Eastern (n=327) and 10 host European (n=849) non-Jewish populations. Only four mtDNA haplogroups (Hgs) (defined on the basis of diagnostic coding region RFLPs and HVS-1 sequence variants) account for approximately 70% of Ashkenazi mtDNA variation. While several Ashkenazi Jewish mtDNA Hgs appear to derive from the Near East, there is also evidence for a low level of introgression from host European non-Jewish populations. HVS-1 sequence analysis revealed increased frequencies of Ashkenazi Jewish haplotypes that are rare or absent in other populations, and a reduced number of singletons in the Ashkenazi Jewish sample. These diversity patterns provide evidence for a prolonged period of low effective size in the history of the Ashkenazi population. The data best fit a model of an early bottleneck (approximately 100 generations ago), perhaps corresponding to initial migrations of ancestral Ashkenazim in the Near East or to Europe. A genetic bottleneck followed by the recent phenomenon of rapid population growth are likely to have produced the conditions that led to the high frequency of many genetic disease alleles in the Ashkenazi population.