Indu Sharma, Varun Sharma, Akbar Khan, Parvinder Kumar, Ekta Rai, Rameshwar N. K. Bamezai, Miguel Vilar & Swarkar Sharma
Jammu and Kashmir (J&K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.
Muthusamy B, Selvan LDN, Nguyen TT, Manoj J, Stawiski EW, Jaiswal BS, Wang W, Raja R, Ramprasad VL, Gupta R, Murugan S, Kadandale JS, Prasad TSK, Reddy K, Peterson A, Pandey A, Seshagiri S, Girimaji SC, Gowda H, OMICS, 2017 May;21(5):295-303.
Robust diagnostics for many human genetic disorders are much needed in the pursuit of global personalized medicine. Next- generation sequencing now offers new promise for biomarker and diagnostic discovery, in developed as well as resource-limited countries. In this broader global health context, X-linked intellectual disability (XLID) is an inherited genetic disorder that is associated with a range of phenotypes impacting societies in both developed and developing countries. Although intellectual disability arises due to diverse causes, a substantial proportion is caused by genomic alterations. Studies have identified causal XLID genomic alterations in more than 100 protein-coding genes located on the X-chromosome. However, the causes for a substantial number of intellectual disability and associated phenotypes still remain unknown. Identification of causative genes and novel mutations will help in early diagnosis as well as genetic counseling of families. Advent of next-generation sequencing methods has accelerated the discovery of new genes involved in mental health disorders. In this study, we analyzed the exomes of three families from India with nonsyndromic XLID comprising seven affected individuals. The affected individuals had varying degrees of intellectual disability, microcephaly, and delayed motor and language milestones. We identified potential causal variants in three XLID genes, including PAK3 (V294M), CASK (complex structural variant), and MECP2 (P354T). Our findings reported in this study extend the spectrum of mutations and phenotypes associated with XLID, and calls for further studies of intellectual disability and mental health disorders with use of next-generation sequencing technologies.
Sunita Bijarnia-Mahay, Deepti Gupta, V L Ramprasad, Sakthivel Murugan, Renu Saxena, Sudha Kohli, Seiji Yamaguchi, Yosuke Shigematsu and I C Verma, Genetic Clinics 2017, January – March, Vol 10, Issue 1.
Next generation sequencing has changed the approach to genetic diagnosis and testing in recent times. The days have arrived when a molecular genetic diagnosis can be attempted even without the availability of the proband or affected person. However this requires additional strong evidence of diagnosis in the proband, such as biochemical or radiological hallmarks. Needless to say, this attempt should always be made during counseling to make the family aware of the fallacies and limitation involved due to non-availability of the sample of the proband. Since many recessive disorders are either fatal or severely debilitating and burdensome, with no easy treatment, the NGS technology has provided a much needed relief in terms of testing and prevention in family by enabling prenatal diagnosis, at least in a few cases. Encouraging results have been shown upon testing of the proband directly. However, the final word remains to be said on complete reliability of the method for carrier testing, performed without availability of the proband. We present two similar cases, of methyl malonic acidemia, where use of NGS resulted in contrasting outcomes after genetic testing for carrier status, thus highlighting the utility and the futility of the test in certain situations. While a correct identification of mutations in the first couple (in the MMAB gene) resulted in successful prenatal diagnosis and prevention of recurrence, an inability to identify the disease and mutation resulted in birth of an affected baby with MMA in the second family.
Sai Rani Karanam, Vinay Kumar Konana, Shruthi Sreenivasaiah, Sudhakar Potti, Delhi Journal of Ophthalmology (2016).
Manitoba-oculo-tricho-anal (MOTA) syndrome is very rare syndrome characterized by aberrant hairline, eye anomalies (ocular hypertelorism, cryptophthalmos, and upper eyelid colobomas), bifid nose, omphalocele and anorectal anomalies. MOTA syndrome was first reported in 1992 in Oji-cree community from the Island Lake region of Manitoba, Canada. Till date very few cases of MOTA have been reported and none from India. We report first case of MOTA syndrome from India. A two month old male baby was brought with complaints of defect in right upper eye lid since birth. He was the second born child of a second degree consanguineously married couple at 37 weeks of gestation. On physical examination, the baby had right upper eyelid coloboma, ocular hypertelorism, bifid nose, small nasal ala and bilateral undescended testis. Investigations revealed high anorectal anomaly and right renal agenesis. Whole exome sequencing showed homozygous nonsense variation in exon 25 of the FREM1 gene that resulted in a stop codon. This case gains importance as it is the first case of MOTA being reported from India and bilateral undescended testis which was seen this case is an addition to the variable clinical spectrum of MOTA.
Aggarwal S, Bhowmik AD, Ramprasad VL, Murugan S, Dalal A, Am J Med Genet A. 2016 Jul;170(7):1868-73.
We report on a sib pair of Indian origin presenting with intellectual disability, dysmorphism, and macrocephaly. Exome sequencing revealed a homozygous splice site HERC1 mutation in both probands. Functional analysis revealed use of an alternate splice site resulting in formation of a downstream stop codon and nonsense mediated decay. In the light of recent reports of HERC1 mutations in two families with a similar phenotypic presentation, this report reiterates the pathogenic nature and clinical consequences of HERC1 disruption.