Molecular defects identified by whole exome sequencing in a child with Fanconi anemia

Fanconi anemia is a rare genetic disease characterized by bone marrow failure, multiple congenital malformations, and an increased susceptibility to malignancy. At least 15 genes have been identified that are involved in the pathogenesis of Fanconi anemia. However, it is still a challenge to assign the complementation group and to characterize the molecular defects in patients with Fanconi anemia. In the current study, whole exome sequencing was used to identify the affected gene(s) in a boy with Fanconi anemia. A recurring, non-synonymous mutation was found (c.3971C>T, p.P1324L) as well as a novel frameshift mutation (c.989_995del, p.H330LfsX2) in FANCA gene. Our results indicate that whole exome sequencing may be useful in clinical settings for rapid identification of disease-causing mutations in rare genetic disorders such as Fanconi anemia.     

Haplotypes of nine single nucleotide polymorphisms on chromosome 19q13.2-3 associated with susceptibility of lung cancer in a Chinese population

To evaluate the joint effect of nine single nucleotide polymorphisms for three DNA repair genes in the region of chromosome 19q13.2-3 on susceptibility of lung cancer in a Chinese population, we conducted a hospital-based case–control study consisting of 247 lung cancer cases and 253 cancer-free controls matched on age, gender and ethnicity. Associations between the haplotypes and susceptibility of lung cancer were tested. The global test of haplotype association revealed a statistically significant difference in the haplotype distribution between cases and controls (global test: χ² = 60.45, d.f. = 15, P = 2.11E−07). The two haplotypes were underrepresented among cases (Hap5 defined by ERCC1118^A–ERCC2156^C–ERCC2312^G–ERCC2751^A–XRCC1194^T–XRCC1206^A–XRCC1280^G–XRCC1399^G–XRCC1632^G and Hap12 defined by ERCC1118^G–ERCC2156^C–ERCC2312^G–ERCC2751^A–XRCC1194^C–XRCC1206^A–XRCC1280^G–XRCC1399^A–XRCC1632^G). Three of the haplotypes were overrepresented among cases (Hap3 defined by ERCC1118^A–ERCC2156^C–ERCC2312^G–ERCC2751^A–XRCC1194^C–XRCC1206^A–XRCC1280^G–XRCC1399^G–XRCC1632^G, Hap4 defined by ERCC1118^A–ERCC2156^C–ERCC2312^G–ERCC2751^A–XRCC1194^C–XRCC1206^G–XRCC1280^G–XRCC1399^G–XRCC1632^A, and Hap10 defined by ERCC1118^G–ERCC2156^A–ERCC2312^G–ERCC2751^A–XRCC1194^T–XRCC1206^A–XRCC1280^G–XRCC1399^G–XRCC1632^G). Haplotypes 3 and 10 (cases = 5.7%, controls = 1.0%, OR = 6.56, 95%CI = 1.83–23.54, P = 0.001; cases = 13.3%, controls = 5.6%, OR = 2.73, 95%CI = 1.51–4.94, P = 0.0006) were the most strongly associated with increased lung cancer risk. There was considerable linkage disequilibrium exists between SNPs both within genes and between genes in the region. The two blocks for solid spine of LD and six htSNPs were found. The haplotype analysis suggested that the biologically effective polymorphisms co-segregate with some of the haplotypes. This result supports the hypothesis that the sub-region is important for lung cancer susceptibility. Haplotype studies using larger study groups will be required to obtain conclusive results.     

Dynamic interactions between RNA viruses and human hosts unravelled by a decade of next generation sequencing

Background

Next generation sequencing (NGS) methods have significantly contributed to a paradigm shift in genomic research for nearly a decade now. These methods have been useful in studying the dynamic interactions between RNA viruses and human hosts.

Genomic diversity and affinities in population groups of North West India: An analysis of Alu insertion and a single nucleotide polymorphism

The North West region of India is extremely important to understand the peopling of India, as it acted as a corridor to the foreign invaders from Eurasia and Central Asia. A series of these invasions along with multiple migrations led to intermixture of variable populations, strongly contributing to genetic variations. The present investigation was designed to explore the genetic diversities and affinities among the five major ethnic groups from North West India; Brahmin, Jat Sikh, Bania, Rajput and Gujjar. A total of 327 individuals of the abovementioned ethnic groups were analyzed for 4 Alu insertion marker loci (ACE, PV92, APO and D1) and a Single Nucleotide Polymorphism (SNP) rs2234693 in the intronic region of the ESR1 gene. Statistical analysis was performed to interpret the genetic structure and diversity of the population groups. Genotypes for ACE, APO, ESR1 and PV92 loci were found to be in Hardy–Weinberg equilibrium in all the ethnic groups, while significant departures were observed at the D1 locus in every investigated population after Bonferroni's correction. The average heterozygosity for all the loci in these ethnic groups was fairly substantial ranging from 0.3927 ± 0.1877 to 0.4333 ± 0.1416. Inbreeding coefficient indicated an overall 10% decrease in heterozygosity in these North West Indian populations. The gene differentiation among the populations was observed to be of the order of 0.013. Genetic distance estimates revealed that Gujjars were close to Banias and Jat Sikhs were close to Rajputs. Overall the study favored the recent division of the populations of North West India into largely endogamous groups. It was observed that the populations of North West India represent a more or less homogenous genetic entity, owing to their common ancestral history as well as geographical proximity.