Study of the association of forkhead box P3 (FOXP3) gene polymorphisms with unexplained recurrent spontaneous abortions in Indian population.

Recurrent spontaneous abortions (RSA) is defined as three or more consecutive pregnancy losses before 20 weeks of gestation. Various causes of RSA have been identified, still 50% cases remain unexplained after evaluation. One of the causes of unexplained recurrent spontaneous abortions (URSA) is supposed to be the disruption of immunological tolerance at foeta-maternal interface. Regulatory T cells (Tregs) are responsible for the development of immune-tolerant environment at foetal-maternal interface and supports pregnancy. Forkhead/winged helix transcription factor (FOXP3) gene plays an important role in the development and function of Tregs. In URSA, Tregs (CD4+CD25+) are reduced in peripheral blood and decidua of pregnant women. This reduction of Tregs (CD4+CD25+) is associated with decreased expression of FOXP3 gene. This study evaluated the association between singlenucleotide polymorphisms (SNPs) in FOXP3 gene and URSA in Indian population. In this study, 100 patients with a history of URSA and 100 healthy ethnically matched women with at least one normal pregnancy and no abortion were included as case and control groups, respectively. Four SNPs of FOXP3 gene, two in the promoter region: -924A/G and -3279C/A, and two intronic, -20G/A and +459T/C, were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). -924A/G and +459T/C polymorphisms were found to be associated with URSA. -3279C/A and -20G/A polymorphism were not found to be associated with URSA. The odds ratio (OR) of mutant allele G for -924A/G polymorphism was 2.5 (95% CI 1.7-3.8; P< 0.001) and mutant allele C for +459T/C polymorphism was 1.7 (95% CI 1.1-2.6; P= 0.01). For -20G/A polymorphism, only GG genotype was found in both URSA and controls. These results suggest that -924A/G and +459T/C polymorphisms of the FOXP3 gene might be associated with URSA and -20G/A polymorphism is likely to be rare in Indian population and might not be associated with URSA.

Hyperekplexia: A forgotten diagnosis clinched by next-generation sequencing.

Hyperekplexia is a rare early neonatal onset, potentially treatable, neurological disorder, characterized by a triad of immediate neonatal-onset stiffness, an exaggerated startle reflex in response to tactile or auditory stimuli followed by short periodical generalized stiffness. It is a monogenic genetically heterogeneous condition which can be potentially life threatening due to apneic episodes and is usually misdiagnosed as seizures. Here, we report two female siblings with hyperekplexia who were being treated by multiple antiepileptic medications for seizure-like episodes. Hyperekplexia was diagnosed by next-generation sequencing, which has emerged as a powerful diagnostic tool over the last few years.

Microarray-based large scale detection of single feature polymorphism in Gossypium hirsutum L.

Microarrays offer an opportunity to explore the functional sequence polymorphism among different cultivars of many crop plants. The Affymetrix microarray expression data of five genotypes of Gossypium hirsutum L. at six different fibre developmental stages was used to identify single feature polymorphisms (SFPs). The background corrected and quantile-normalized log2 intensity values of all probes of triplicate data of each cotton variety were subjected to SFPs call by using SAM procedure in R language software. We detected a total of 37,473 SFPs among six pair genotype combinations of two superior (JKC777 and JKC725) and three inferior (JKC703, JKC737 and JKC783) using the expression data. The 224 SFPs covering 51 genes were randomly selected from the dataset of all six fibre developmental stages of JKC777 and JKC703 for validation by sequencing on a capillary sequencer. Of these 224 SFPs, 132 were found to be polymorphic and 92 monomorphic which indicate that the SFP prediction from the expression data in the present study confirmed a ~58.92% of true SFPs. We further identified that most of the SFPs are associated with genes involved in fatty acid, flavonoid, auxin biosynthesis etc. indicating that these pathways significantly involved in fibre development.

Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.).

Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.