SummaryIsolated population groups are useful in conducting association studies of complex diseases to avoid various pitfalls, including those arising from population stratification. Since DNA resequencing is expensive, it is recommended that genotyping be carried out at tagSNP (tSNP) loci. For this, tSNPs identified in one isolated population need to be used in another. Unless tSNPs are highly portable across populations this strategy may result in loss of information in association studies. We examined the issue of tSNP portability by sampling individuals from 10 isolated ethnic groups from India. We generated DNA resequencing data pertaining to 3 genomic regions and identified tSNPs in each population. We defined an index of tSNP portability and showed that portability is low across isolated Indian ethnic groups. The extent of portability did not significantly correlate with genetic similarity among the populations studied here. We also analyzed our data with sequence data from individuals of African and European descent. Our results indicated that it may be necessary to carry out resequencing in a small number of individuals to discover SNPs and identify tSNPs in the specific isolated population in which a disease association study is to be conducted.

This study reports results of an extensive and comprehensive study of genetic diversity in 12 genes of the innate immune system in a population of eastern India. Genomic variation was assayed in 171 individuals by resequencing ~75 kb of DNA comprising these genes in each individual. Almost half of the 548 DNA variants discovered was novel. DNA sequence comparisons with human and chimpanzee reference sequences revealed evolutionary features indicative of natural selection operating among individuals, who are residents of an area with a high load of microbial and other pathogens. Significant differences in allele and haplotype frequencies of the study population were observed with the HapMap populations. Gene and haplotype diversities were observed to be high. The genetic positioning of the study population among the HapMap populations based on data of the innate immunity genes substantially differed from what has been observed for Indian populations based on data of other genes. The reported range of variation in SNP density in the human genome is one SNP per 1.19 kb (chromosome 22) to one SNP per 2.18 kb (chromosome 19). The SNP density in innate immunity genes observed in this study (>3 SNPs kb −1 ) exceeds the highest density observed for any autosomal chromosome in the human genome. The extensive genomic variation and the distinct haplotype structure of innate immunity genes observed among individuals have possibly resulted from the impact of natural selection.

Glioblastoma multiforme (GBM) is the most prevalent central nervous system malignancy portending dismal prognosis. The median overall survival (OS) is 14.6 months with currently available standard care of surgery, radiotherapy and Temozolomide (TMZ) chemotherapy. TMZ, which is the best chemotherapeutic drug till date for this malignancy, gives a median OS advantage of only 2.5 months over surgery and radiotherapy alone. It is not clear how the benefit of TMZ is severely limited in a large majority of patients. To understand this we investigated genome wide sequence alterations of GBM neoplastic cells in response to TMZ. We present here two cases of GBM, A49910 and M45481, where the first one (A49910) showed response and the second one (M45481) showed no response to standard treatment in clinic. We isolated their primary tumor cells at the time of surgery and cultured them in vitro as neurospheres. When we exposed these two patient-derived neurospheres to clinically relevant dose of TMZ in vitro differential responses were observed among the two neurospheres which mirrored the clinical outcomes of the two patients respectively. Initially, at the end of 5 days of TMZ treatment, both A49910 and M45481 neurospheres showed 50% and 65% reduction in viable cell numbers respectively but after a 23 days of gap (“post TMZ-treatment recovery” from the 5 days long drug treatment), at 28th day of the treatment cycle, the total number of viable cells was 5% in TMZ-treated A49910 with a stark contrast of 60% in the TMZ-treated M45481 as compared to their respective DMSO-treated controls. Their growth curves, as measured by MTT assays, showed the exact reflection of this pattern, i.e., after 5 days of treatment both TMZ-treated A49910 and TMZ-treated M45481 showed equally retarded growth compared to their DMSO-treated controls, and at 28th day, only the TMZ-treated A49910 but not the TMZ-treated M45481 cells showed growth retardation. Moreover, almost every single cell of TMZ-treated A49910 appeared bigger and stained intensely with SA-βgal confirming drug induced senescence at 28th day whereas this phenotype was completely absent in TMZ-treated M45481, where no apparent sign of senescence was observed. However, apoptosis was two-fold higher in M45481 than in A49910 after 5 days of TMZ treatment. Whether this “drug induced cellular senescence (DICS)” phenotype is more beneficial to the patients claims further investigation with a larger cohort of GBM patients. For the proof of principle we sequenced the whole exome and also analyzed the genome wide single nucleotide polymorphisms (SNPs, intronic and exonic) in these two patient-derived neurospheres before and after TMZ treatment in vitro and detected a list of unique sequence alterations in both the cases, in response to TMZ. Citation Format: Neeta Sarkar Roy, Nidhan Biswas, Vikas Chandra, Tapojyoti Das, Ankita Chatterjee, Rabindra Narayan Bhattacharya, Laxminarayan Tripathy, Sunandan Basu, Arindam Maitra, Pryiadarshi Basu, Analabha Basu, Surajit Dhara. How important is the “post TMZ-treatment recovery” of GBM neoplastic cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3430. doi:10.1158/1538-7445.AM2013-3430