The promise of discovering population-specific disease-associated genes in South Asia

The more than 1.5 billion people who live in South Asia are correctly viewed not as a single large population but as many small endogamous groups. We assembled genome-wide data from over 2,800 individuals from over 260 distinct South Asian groups. We identified 81 unique groups, 14 of which had estimated census sizes of more than 1 million, that descend from founder events more extreme than those in Ashkenazi Jews and Finns, both of which have high rates of recessive disease due to founder events. We identified multiple examples of recessive diseases in South Asia that are the result of such founder events. This study highlights an underappreciated opportunity for decreasing disease burden among South Asians through discovery of and testing for recessive disease-associated genes.

Analysis of genotype and haplotype effects of ABCB1 (MDR1) polymorphisms in the risk of medically refractory epilepsy in an Indian population

The transmembrane P-glycoprotein that functions as a drug-efflux transporter coded by ATP-binding cassette, subfamily B, member 1/Multidrug Resistance 1 (ABCB1/MDR1) gene is considered relevant to drug absorption and elimination, with access to the central nervous system. Effects of three ABCB1 single nucleotide polymorphisms (SNPs) in genotypic and haplotypic combination have been evaluated in a south Indian population for risk of pediatric medically refractory epilepsy. The study included age and sex matched medically refractory (N=113) cases and drug responsive epilepsy patients (N=129) as controls, belonging to the same ethnic population recruited from a tertiary referral centre, of Karnataka, Southern India. The genotype frequencies of SNPs c.1236C>T, c.2677G>T/A, and c.3435C>T were determined from genomic DNA of the cases and controls by PCR- RFLP and confirmatory DNA sequencing. 256 normal population samples of the same ethnicity were genotyped for the three loci to check for population stratification. Results indicate that there was no statistically significant difference between allele and genotype frequencies of refractory and drug responsive epilepsy patients. The predicted haplotype frequencies of the three polymorphisms did not show significant difference between cases and controls. The results confirm earlier observations on absence of association of ABCB1 polymorphisms with medically refractory epilepsy.

Simultaneous detection of periodontal pathogens in subgingival plaque and placenta of women with hypertension in pregnancy

BACKGROUND

There are many studies documenting increased prevalence of periodontal infection in women with preeclampsia. But, very few studies have attempted to establish causal relationship between the two.

OBJECTIVE

To find out causal circumstantial evidence by isolating specific periodontal pathogens in oral and placental samples.

MATERIALS AND METHODS

Antenatal periodontal screening and subgingival plaque collection was carried out in ten women with hypertension in pregnancy and ten normotensive controls on their hospital admission at term for cesarean delivery. Placental biopsy was obtained after aseptic placental collection at the time of elective cesarean delivery. Subgingival plaque and placental biopsy were studied for Porphyromonas gingivalis, Fusobacterium nucleatum, Treponema denticola, Prevotella intermedia and Aggregatibacter actinomycetemcomitans using quantitative polymerase chain reaction technique. Periodontist and laboratory personnel were unaware of case or control status. Periodontal status was not informed to the obstetrician recruiting the cases and laboratory. Microbiology report was not revealed till end of the study.

RESULTS

Periodontal pathogens were found to be high in the group with hypertension than the controls. P gingivalis was found in all the samples from subgingival plaque and placenta, irrespective of the periodontal disease status.

CONCLUSION

In cases with hypertension, periodontal pathogens are present in higher proportion in subgingival plaque and placenta.

Thiopurine S-methyltransferase alleles, TPMT(*)2, (*)3B and (*)3C, and genotype frequencies in an Indian population

Thiopurine S-methyltransferase (TPMT) catalyzes the S-methylation of aromatic and heterocyclic sulfhydryl compounds including thiopurine drugs such as 6-mercaptopurine, 6-thioguanine and azathioprine. TPMT activity exhibits genetic variation and shows tri-modal distribution with 89-94% of individuals possessing high activity, 6-11% intermediate activity and approximately 0.3% low activity. Patients with intermediate or deficient TPMT activity exposed to thiopurine drugs show severe hematopoietic toxicity. Three single nucleotide polymorphisms (SNPs) in TPMT (NM_000367.2:c.238G>C, NM_000367.2:c.460G>A and NM_000367.2:c.719A>G) define the most prevalent mutant alleles associated with loss of catalytic activity reported in several populations. The present study investigated, for the first time, the frequency distribution of these three SNPs of TPMT, their alleles and genotypes in a Southern Indian population. Peripheral blood was obtained from 326 individuals of a Southern Indian population, and genomic DNA was isolated from total peripheral white blood cells. The genotypes at the polymorphic loci were determined by allele-specific polymerase chain reaction, restriction fragment length polymorphism and confirmatory DNA sequencing. The estimated genotype frequency for homozygous TPMT(*)1/(*)1 was 97.24%, for heterozygous TPMT(*)1/(*)2 and TPMT(*)1/(*)3B, 0.61% each, and for heterozygous TPMT(*)1/(*)3C, 1.53%. The frequency of heterozygous mutants in the studied Indian population was 2.76%. This study demonstrated significant variations in TPMT gene polymorphisms in an Indian population in relation to other human populations and may help to predict both clinical efficacy and drug toxicity of thiopurine drugs.

EVALUATION OF MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION AS A TOOL FOR DIAGNOSIS AND CARRIER DETECTION IN FAMILIES WITH A DYSTROPHINOPATHY

We set out to evaluate multiplex ligation dependent probe amplification (MLPA) as a tool for diagnosis and carrier detection in families with a dystrophinopathy. Fifty three Indian families with provisional diagnosis of Duchene muscular dystrophy or Becker muscular dystrophy were evaluated by MLPA and multiplex polymerase chain reaction (PCR). Sanger sequencing was used to analyze the entire gene in one patient. Mothers were tested for carrier status whenever possible. Molecular analysis of DMD gene by combining MLPA and multiplex PCR yielded a mutation detection rate of 62% (33/53). Deletions were detected in 27/53 (51%) cases, duplications in 5/53 (9%) cases, a small deletion one case and Sanger sequencing detected a nonsense mutation in one case. Mutation was not detected in 36% (19/53) cases. Fifty six percent of mothers (9/16) were found to be carriers. MLPA helped to refine the results of multiplex PCR testing in 22 patients (5 duplications, 16 deletions and one small deletion). We also describe a situation where a deletion of single exon on MLPA (but not detected by multiplex PCR) was actually due to a deletion of two nucleotides in the probe ligation site. MLPA appears to score over multiplex PCR in diagnosis and carrier detection, specifically by detecting deletions and duplications that are not detected by traditional multiplex PCR.

Correction to: Simultaneous detection of periodontal pathogens in subgingival plaque and placenta of women with hypertension in pregnancy

The original version of this article unfortunately contained a mistake. Ambika Devi K was not listed among the authors. The corrected authorship is given below.