Evaluation of next-generation sequencing software in mapping and assembly
We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving. We then compared the performance of several programs in these two fields and further provided advices on selecting suitable tools for specific biological applications. (Source: Journal of Human Genetics)
Source: Journal of Human Genetics - June 16, 2011 Category: Genetics & Stem Cells Source Type: research
PTPN11, SOS1, KRAS, and RAF1 gene analysis, and genotype –phenotype correlation in Korean patients with Noonan syndrome
AbstractAfter 2006, germline mutations in theKRAS,SOS1, andRAF1 genes were reported to cause Noonan syndrome (NS), in addition to thePTPN11 gene, and now we can find the etiology of disease in approximately 60 –70% of NS cases. The aim of this study was to assess the correlation between phenotype and genotype by molecular analysis of thePTPN11,SOS1,KRAS, andRAF1 genes in 59 Korean patients with NS. We found disease-causing mutations in 30 (50.8%) patients, which were located in thePTPN11 (27.1%),SOS1 (16.9%),KRAS (1.7%), andRAF1 (5.1%) genes. Three novel mutations (T59A inPTPN11, K170E inSOS1, S259T inRAF1) were identifi...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Genetic variants of FOXA2 : risk of type 2 diabetes and effect on metabolic traits in North Indians
AbstractHere, we examined the association of genetic variants ofFOXA2, an upstream activator of the β-cell transcription factor network, with type 2 diabetes and related phenotypes in North India. We genotyped three SNPs (rs1212275, rs1055080, rs6048205) and the (TCC)n repeat polymorphism in 1,656 participants comprising 1,031 patients with type 2 diabetes and 625 controls. SNPs rs1212275 and rs6048205 were uncommon (MAF < 5%) with similar distribution among patients and controls. We found a strong association of (TCC)n common allele A5 with type 2 diabetes [OR = 1.66 (95% CI 1.36–2.04,p = 5.9 × 10−7) f...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Common coding variant in the TCF7L2 gene and study of the association with type 2 diabetes in Japanese subjects
AbstractGenetic variants of the transcription factor 7-like 2 (TCF7L2) gene affect the risk of type 2 diabetes in populations with multiple ethnic groups. However, a comprehensive survey of this gene has not been done for a Japanese population. Thus, we conducted this gene-based association study, in which the common genetic variants were analyzed. Using 24 Japanese type 2 diabetic subjects, we first screened a 9.5 kb region, which included the entire coding sequence, to assess potential functional variants of TCF7L2. Sequencing revealed a common coding variant (Pro477Thr) in exon 14 of TCF7L2 that was not enrolled in th...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Association study to evaluate the serotonin transporter and apolipoprotein E genes in frontotemporal lobar degeneration in Italy
AbstractFrontotemporal lobar degeneration (FTLD) is a progressive neurodegenerative disorder characterized by behavioral and language disturbances. We performed a case-control association study in the Italian population to assess the relevance for FTLD genetic susceptibility of the serotonin (5-HT) transporter gene-linked polymorphic region [rs4795541, alias short (S)/long (L)] an in/del polymorphism of the promoter region of the gene coding for the 5-HT transporter (SLC6A4). This functional polymorphism was reported to influence theSLC6A4 transcription rate, with the S-allele having a two-fold reduced efficiency. We colle...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Molecular basis of complement factor I (CFI) polymorphism: one of two polymorphic suballeles responsible for CFI A is Japanese-specific
In this study the molecular basis of the CFI polymorphism was investigated in 174 Japanese. TheCFI*A was divided into two suballeles,CFI*As (R201S) andCFI*Ah (R406H).CFI*Aj, a rare variant allele originating fromCFI*Ah, had an additional mutation (R502L). The distribution of these three mutations and two registered SNPs was investigated in a total of 2,471 individuals in 20 populations from various areas, and six haplotypes were observed. Haplotype H3, which is characterized byCFI*As, was found only in Far East populations: the frequencies were about 0.03 in the main island of Japan and lower than 0.01 in Okinawa and Korea...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Association between polymorphisms in SLC30A8 , HHEX , CDKN2A/B , IGF2BP2 , FTO , WFS1 , CDKAL1 , KCNQ1 and type 2 diabetes in the Korean population
In conclusion, we have shown that SNPs inHHEX,CDKN2A/B,CDKAL1,KCNQ1 andSLC30A8 confer a risk of T2DM in the Korean population. (Source: Journal of Human Genetics)
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
An FBN1 pseudoexon mutation in a patient with Marfan syndrome: confirmation of cryptic mutations leading to disease
AbstractMarfan syndrome (MFS) results from heterozygous mutations inFBN1. However, genetic analyses of deoxyribonucleic acid (DNA) from approximately 10 –30% of MFS patients who meet diagnostic criteria do not reveal an identifiableFBN1 mutation. In a patient who met the diagnostic criteria for MFS, bidirectional DNA sequencing of exons and intron –exon boundaries ofFBN1 failed to reveal a mutation. Assessment of theFBN1 message in dermal fibroblasts from the patient revealed insertion of a pseudoexon between exons 63 and 64. Sequencing of intron 63 identified a point mutation, IVS63+373, located near the middle of int...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
PTPN11 , SOS1 , KRAS , and RAF1 gene analysis, and genotype –phenotype correlation in Korean patients with Noonan syndrome
AbstractAfter 2006, germline mutations in theKRAS,SOS1, andRAF1 genes were reported to cause Noonan syndrome (NS), in addition to thePTPN11 gene, and now we can find the etiology of disease in approximately 60 –70% of NS cases. The aim of this study was to assess the correlation between phenotype and genotype by molecular analysis of thePTPN11,SOS1,KRAS, andRAF1 genes in 59 Korean patients with NS. We found disease-causing mutations in 30 (50.8%) patients, which were located in thePTPN11 (27.1%),SOS1 (16.9%),KRAS (1.7%), andRAF1 (5.1%) genes. Three novel mutations (T59A inPTPN11, K170E inSOS1, S259T inRAF1) were identifi...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
LRRK2 P755L variant in sporadic Parkinson ’s disease
AbstractParkinson ’s disease (PD) is a neurodegenerative disorder of unknown etiology with probable involvement of genetic-environmental factors. The majority of PD cases (approximately 90–95%) are sporadic, while familial cases account for approximately 5–10% of PD. In a recent report, a heterozygousLRRK2 P755L mutation withinLRRK2 exon 19 was found in 2% of Chinese sporadic PD patients and in 0% of normal controls or Caucasians, suggesting that the mutation is disease-associated with ethnic specificity. To further evaluate the role ofLRRK2 P755L variant in sporadic PD, we performed direct sequencing ofLRRK2 exon 19...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Nonparametric estimation of LOH using Affymetrix SNP genotyping arrays for unpaired samples
AbstractStudies of loss of heterozygosity (LOH) play an important role in cancer research. In this paper, we developed a two-step procedure to examine LOH by comparing unpaired tumour and normal samples. In the first step we determined which chromosomes significantly differ between the two sets of samples by using nonparametric procedures. We then used the biplot data visualisation technique and homozygosity intensity estimates to determine the regions of these chromosomes that required further examination. We illustrated our method by examining 22 autosomes in samples of 95 normal controls and 14 acute lymphoblastic leuka...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Association of the SLC45A2 gene with physiological human hair colour variation
AbstractPigmentation is a complex physical trait with multiple genes involved. Several genes have already been associated with natural differences in human pigmentation. The SLC45A2 gene encoding a transporter protein involved in melanin synthesis is considered to be one of the most important genes affecting human pigmentation. Here we present results of an association study conducted on a population of European origin, where the relationship between two non-synonymous polymorphisms in the SLC45A2 gene — rs26722 (E272K) and rs16891982 (L374F) — and different pigmentation traits was examined. The study revealed a signif...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Carrier frequency of GJB2 (connexin-26) mutations causing inherited deafness in the Korean population
AbstractMutations in theGJB2 gene are associated with hereditary hearing loss. Although most studies ofGJB2 mutations have dealt with hearing-impaired patients, there are few reports of the frequency of these mutations in the general population. The purpose of this study is to evaluate the prevalence ofGJB2 mutations causing inherited deafness in the general Korean population. Blood samples were obtained from 2,072 newborns with normal hearing. The dried blood samples were subjected to PCR to amplify the entire coding region of theGJB2 gene, which was followed by direct DNA sequencing. A total of 24 different sequence vari...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Genetic variants of FOXA2 : risk of type 2 diabetes and effect on metabolic traits in North Indians
Abstract
Here, we examined the association of genetic variants of FOXA2, an upstream activator of the β-cell transcription factor network, with type 2 diabetes and related phenotypes in North India. We genotyped three SNPs (rs1212275, rs1055080, rs6048205) and the (TCC)
n
repeat polymorphism in 1,656 participants comprising 1,031 patients with type 2 diabetes and 625 controls. SNPs rs1212275 and rs6048205 were uncommon (MAF < 5%) with similar distribution among patients and controls. We found a strong association of (TCC)
n
...
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
Association between polymorphisms in SLC30A8 , HHEX , CDKN2A/B , IGF2BP2 , FTO , WFS1 , CDKAL1 , KCNQ1 and type 2 diabetes in the Korean population
In conclusion, we have shown that SNPs in HHEX, CDKN2A/B, CDKAL1, KCNQ1 and SLC30A8 confer a risk of T2DM in the Korean population. (Source: Journal of Human Genetics)
Source: Journal of Human Genetics - December 1, 2008 Category: Genetics & Stem Cells Source Type: research
