REFERENCES
Aggarwal, S., Gheware, A., Agrawal,
A., Ghosh, S., Prasher, B., & Mukerji, M. (2015). Combined genetic
effects of EGLN1 and VWF modulate thrombotic outcome in hypoxia revealed
by Ayurgenomics approach. Journal of translational medicine,
13 (1), 184.
Aggarwal, S., Negi, S., Jha, P.,
Singh, P. K., Stobdan, T., Pasha, M. Q., . . . Mukerji, M. (2010). EGLN1
involvement in high-altitude adaptation revealed through genetic
analysis of extreme constitution types defined in Ayurveda.Proceedings of the National Academy of Sciences, 107 (44),
18961-18966.
Ahmed P, H., More, R. P., Viswanath,
B., Jain, S., Rao, M. S., Mukherjee, O., & Consortium, A. (2019).
INDEX-db: The Indian Exome Reference Database (Phase I). Journal
of Computational Biology, 26 (3), 225-234.
Alves, M. M., Sribudiani, Y., Brouwer,
R. W., Amiel, J., Antiñolo, G., Borrego, S., . . . Garcia-Barcelo, M.-M.
(2013). Contribution of rare and common variants determine complex
diseases—Hirschsprung disease as a model. Developmental biology,
382 (1), 320-329.
Azad, A. K., Sadee, W., &
Schlesinger, L. S. (2012). Innate immune gene polymorphisms in
tuberculosis. Infection and immunity, 80 (10), 3343-3359.
Bamshad, M., Kivisild, T., Watkins, W.
S., Dixon, M. E., Ricker, C. E., Rao, B. B., . . . Rasanayagam, A.
(2001). Genetic evidence on the origins of Indian caste populations.Genome research, 11 (6), 994-1004.
Bancone, G., Chu, C. S.,
Somsakchaicharoen, R., Chowwiwat, N., Parker, D. M., Charunwatthana, P.,
. . . Nosten, F. H. (2014). Characterization of G6PD genotypes and
phenotypes on the northwestern Thailand-Myanmar border. PloS one,
9 (12), e116063.
Basu, A., Mukherjee, N., Roy, S.,
Sengupta, S., Banerjee, S., Chakraborty, M., . . . Bhattacharyya, N. P.
(2003). Ethnic India: a genomic view, with special reference to peopling
and structure. Genome research, 13 (10), 2277-2290.
Basu, A., Sarkar-Roy, N., & Majumder,
P. P. (2016). Genomic reconstruction of the history of extant
populations of India reveals five distinct ancestral components and a
complex structure. Proceedings of the National Academy of
Sciences, 113 (6), 1594-1599.
Bhattacharjee, A., Banerjee, D.,
Mookherjee, S., Acharya, M., Banerjee, A., Ray, A., . . . Consortium, I.
G. V. (2008). Leu432Val polymorphism in CYP1B1 as a susceptible factor
towards predisposition to primary open-angle glaucoma. Molecular
vision, 14 , 841.
Biswas, A., Maulik, M., Das, S.,
Consortium, I. G. V., Ray, K., & Ray, J. (2007). Parkin polymorphisms:
risk for Parkinson’s disease in Indian population. Clinical
genetics, 72 (5), 484-486.
Biswas, A., Sadhukhan, T., Majumder,
S., Misra, A. K., Das, S. K., Ray, K., . . . Consortium, I. G. V.
(2010). Evaluation of PINK1 variants in Indian Parkinson’s disease
patients. Parkinsonism & related disorders, 16 (3), 167-171.
Borkar, M., Ahmad, F., Khan, F., &
Agrawal, S. (2011). Paleolithic spread of Y-chromosomal lineage of
tribes in eastern and northeastern India. Annals of human biology,
38 (6), 736-746.
Cao, Y., Wang, X., Cao, Z., Wu, C.,
Wu, D., & Cheng, X. (2018). Genetic polymorphisms of MBL2 and
tuberculosis susceptibility: a meta-analysis of 22 case-control studies.Archives of medical science: AMS, 14 (6), 1212.
Chaki, M., Sengupta, M., Mondal, M.,
Bhattacharya, A., Mallick, S., Bhadra, R., & Ray, K. (2011). Molecular
and functional studies of tyrosinase variants among Indian
oculocutaneous albinism type 1 patients. The Journal of
investigative dermatology, 131 (1), 260-262.
Chang, C. C., Chow, C. C., Tellier,
L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015).
Second-generation PLINK: rising to the challenge of larger and richer
datasets. Gigascience, 4 (1), 7.
Consortium, G. P. (2015). A global
reference for human genetic variation. Nature, 526 (7571), 68.
Consortium, I. G. V. (2008). Genetic
landscape of the people of India: a canvas for disease gene exploration.Journal of genetics, 87 (1), 3-20.
Daya, M., Van der Merwe, L., Van
Helden, P. D., Möller, M., & Hoal, E. G. (2015). Investigating the role
of gene-gene interactions in TB susceptibility. PloS one, 10 (4),
e0123970.
Firdous, P., Nissar, K., Ali, S.,
Ganai, B. A., Shabir, U., Hassan, T., & Masoodi, S. R. (2018). Genetic
testing of maturity-onset diabetes of the young current status and
future perspectives. Frontiers in endocrinology, 9 .
GenomeAsia100K Consortium (2019). The GenomeAsia 100K Project enables
genetic discoveries across Asia.Nature. Dec;576(7785):106-111.
Giri, A. K., Khan, N. M., Grover, S.,
Kaur, I., Basu, A., Tandon, N., . . . Brahmachari, S. K. (2014). Genetic
epidemiology of pharmacogenetic variations in CYP2C9, CYP4F2 and VKORC1
genes associated with warfarin dosage in the Indian population.Pharmacogenomics, 15 (10), 1337-1354.
Grillet, N., Schwander, M.,
Hildebrand, M. S., Sczaniecka, A., Kolatkar, A., Velasco, J., . . .
Kimberling, W. J. (2009). Mutations in LOXHD1, an evolutionarily
conserved stereociliary protein, disrupt hair cell function in mice and
cause progressive hearing loss in humans. The American Journal of
Human Genetics, 85 (3), 328-337.
Grover, S., Gourie-Devi, M., Baghel,
R., Sharma, S., Bala, K., Gupta, M., . . . Kaur, K. (2010). Genetic
profile of patients with epilepsy on first-line antiepileptic drugs and
potential directions for personalized treatment. Pharmacogenomics,
11 (7), 927-941.
Gupta, A., Maulik, M., Nasipuri, P.,
Chattopadhyay, I., Das, S. K., Gangopadhyay, P. K., & Ray, K. (2007).
Molecular diagnosis of Wilson disease using prevalent mutations and
informative single-nucleotide polymorphism markers. Clinical
chemistry, 53 (9), 1601-1608.
Hamosh, A., Scott, A. F., Amberger,
J. S., Bocchini, C. A., & McKusick, V. A. (2005). Online Mendelian
Inheritance in Man (OMIM), a knowledgebase of human genes and genetic
disorders. Nucleic acids research, 33 (suppl_1), D514-D517.
Hariprakash, J. M., Vellarikkal, S.
K., Verma, A., Ranawat, A. S., Jayarajan, R., Ravi, R., . . . Kashyap,
A. K. (2018). SAGE: a comprehensive resource of genetic variants
integrating South Asian whole genomes and exomes. Database, 2018 .
Huang, K.-l., Mashl, R. J., Wu, Y.,
Ritter, D. I., Wang, J., Oh, C., . . . Oak, N. (2018). Pathogenic
germline variants in 10,389 adult cancers. Cell, 173 (2), 355-370.
e314.
Jha, A. N., Sundaravadivel, P.,
Singh, V. K., Pati, S. S., Patra, P. K., Kremsner, P. G., . . .
Thangaraj, K. (2014). MBL2 variations and malaria susceptibility in
Indian populations. Infection and immunity, 82 (1), 52-61.
Jha, P., Sinha, S., Kanchan, K.,
Qidwai, T., Narang, A., Singh, P. K., . . . Sharma, S. K. (2012).
Deletion of the APOBEC3B gene strongly impacts susceptibility to
falciparum malaria. Infection, Genetics and Evolution, 12 (1),
142-148.
Kanchan, K., Pati, S., Mohanty, S.,
Mishra, S., Sharma, S., Awasthi, S., . . . Consortium, I. G. V. (2015).
Polymorphisms in host genes encoding NOSII, C-reactive protein, and
adhesion molecules thrombospondin and E-selectin are risk factors for
Plasmodium falciparum malaria in India. European Journal of
Clinical Microbiology & Infectious Diseases, 34 (10), 2029-2039.
Kapoor, S., & Kabra, M. (2010).
Newborn screening in India: Current perspectives. Indian
pediatrics, 47 (3), 219-224.
Karczewski, K., & Francioli, L.
(2017). The Genome Aggregation Database (gnomAD). MacArthur Lab .
Karczewski, K. J., Weisburd, B.,
Thomas, B., Solomonson, M., Ruderfer, D. M., Kavanagh, D., . . .
Cummings, B. B. (2016). The ExAC browser: displaying reference data
information from over 60 000 exomes. Nucleic acids research,
45 (D1), D840-D845.
Kivisild, T., Rootsi, S., Metspalu,
M., Mastana, S., Kaldma, K., Parik, J., . . . Stepanov, V. (2003). The
genetic heritage of the earliest settlers persists both in Indian tribal
and caste populations. The American Journal of Human Genetics,
72 (2), 313-332.
Kumar, J., Garg, G., Kumar, A.,
Sundaramoorthy, E., Sanapala, K. R., Ghosh, S., . . . Sengupta, S.
(2009). Single nucleotide polymorphisms in homocysteine metabolism
pathway genes: association of CHDH A119C and MTHFR C677T with
hyperhomocysteinemia. Circulation: Cardiovascular Genetics, 2 (6),
599-606.
Landrum, M. J., Lee, J. M., Benson,
M., Brown, G., Chao, C., Chitipiralla, S., . . . Hoover, J. (2015).
ClinVar: public archive of interpretations of clinically relevant
variants. Nucleic acids research, 44 (D1), D862-D868.
Lim, R. M., Silver, A. J., Silver, M.
J., Borroto, C., Spurrier, B., Petrossian, T. C., . . . Silver, L. M.
(2016). Targeted mutation screening panels expose systematic population
bias in detection of cystic fibrosis risk. Genetics in medicine,
18 (2), 174.
Majumder, P. P., Roy, B., Banerjee,
S., Chakraborty, M., Dey, B., Mukherjee, N., . . . Sil, S. K. (1999).
Human-specific insertion/deletion polymorphisms in Indian populations
and their possible evolutionary implications. European Journal of
Human Genetics, 7 (4), 435.
Mohan, V., Radha, V., Nguyen, T. T.,
Stawiski, E. W., Pahuja, K. B., Goldstein, L. D., . . . Bhangale, T.
(2018). Comprehensive genomic analysis identifies pathogenic variants in
maturity-onset diabetes of the young (MODY) patients in South India.BMC medical genetics, 19 (1), 22.
Mungall, C. J., McMurry, J. A.,
Köhler, S., Balhoff, J. P., Borromeo, C., Brush, M., . . . Engelstad, M.
(2016). The Monarch Initiative: an integrative data and analytic
platform connecting phenotypes to genotypes across species.Nucleic acids research, 45 (D1), D712-D722.
Nair, V. V., Chapla, A., Arulappan,
N., & Thomas, N. (2013). Molecular diagnosis of maturity onset diabetes
of the young in India. Indian journal of endocrinology and
metabolism, 17 (3), 430.
Narang, A., Jha, P., Rawat, V.,
Mukhopadhayay, A., Dash, D., Basu, A., . . . Consortium, I. G. V.
(2011). Recent admixture in an Indian population of African ancestry.The American Journal of Human Genetics, 89 (1), 111-120.
Narang, A., Roy, R. D., Chaurasia,
A., Mukhopadhyay, A., Mukerji, M., & Dash, D. (2010). IGVBrowser–a
genomic variation resource from diverse Indian populations.Database, 2010 .
Noone, P. G., & Knowles, M. R.
(2001). ’CFTR-opathies’: disease phenotypes associated with cystic
fibrosis transmembrane regulator gene mutations. Respiratory
research, 2 (6), 328.
Peter, B., Wijsman, E. M., Nato Jr,
A. Q., Matsushita, M. M., Chapman, K. L., Stanaway, I. B., . . .
Raskind, W. H. (2016). Genetic candidate variants in two
multigenerational families with childhood apraxia of speech. PloS
one, 11 (4), e0153864.
Pradhan, S., Sengupta, M., Dutta, A.,
Bhattacharyya, K., Bag, S. K., Dutta, C., & Ray, K. (2010). Indian
genetic disease database. Nucleic acids research, 39 (suppl_1),
D933-D938.
Prasher, B., Varma, B., Kumar, A.,
Khuntia, B. K., Pandey, R., Narang, A., . . . Kukreti, R. (2017).
Ayurgenomics for stratified medicine: TRISUTRA consortium initiative
across ethnically and geographically diverse Indian populations.Journal of ethnopharmacology, 197 , 274-293.
Price, A. L., Patterson, N. J.,
Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006).
Principal components analysis corrects for stratification in genome-wide
association studies. Nature genetics, 38 (8), 904.
Reich, D., Thangaraj, K., Patterson,
N., Price, A. L., & Singh, L. (2009). Reconstructing Indian population
history. Nature, 461 (7263), 489.
Sarker, S. K., Islam, M. T., Eckhoff,
G., Hossain, M. A., Qadri, S. K., Muraduzzaman, A., . . . Tahura, S.
(2016). Molecular analysis of Glucose-6-phosphate dehydrogenase gene
mutations in Bangladeshi individuals. PloS one, 11 (11), e0166977.
Sengupta, D., Choudhury, A., Basu,
A., & Ramsay, M. (2016). Population stratification and
underrepresentation of Indian subcontinent genetic diversity in the 1000
genomes project dataset. Genome biology and evolution, 8 (11),
3460-3470.
Shah, A. M., Tamang, R., Moorjani,
P., Rani, D. S., Govindaraj, P., Kulkarni, G., . . . Reddy, A. G.
(2011). Indian siddis: African descendants with Indian admixture.The American Journal of Human Genetics, 89 (1), 154-161.
Sinha, S., Arya, V., Agarwal, S., &
Habib, S. (2009). Genetic differentiation of populations residing in
areas of high malaria endemicity in India. Journal of genetics,
88 (1), 77-80.
Sinha, S., Qidwai, T., Kanchan, K.,
Anand, P., Jha, G. N., Pati, S. S., . . . Sharma, S. K. (2008).
Variations in host genes encoding adhesion molecules and susceptibility
to falciparum malaria in India. Malaria journal, 7 (1), 250.
Sosnay, P. R., Siklosi, K. R., Van
Goor, F., Kaniecki, K., Yu, H., Sharma, N., . . . Zielenski, J. (2013).
Defining the disease liability of variants in the cystic fibrosis
transmembrane conductance regulator gene. Nature genetics,
45 (10), 1160.
Stephens, M., Smith, N. J., &
Donnelly, P. (2001). A new statistical method for haplotype
reconstruction from population data. The American Journal of Human
Genetics, 68 (4), 978-989.
Talwar, P., Kanojia, N., Mahendru,
S., Baghel, R., Grover, S., Arora, G., . . . Singh, M. (2017). Genetic
contribution of CYP1A1 variant on treatment outcome in epilepsy
patients: a functional and interethnic perspective. The
pharmacogenomics journal, 17 (3), 242.
Thanseem, I., Thangaraj, K., Chaubey,
G., Singh, V. K., Bhaskar, L. V., Reddy, B. M., . . . Singh, L. (2006).
Genetic affinities among the lower castes and tribal groups of India:
inference from Y chromosome and mitochondrial DNA. BMC genetics,
7 (1), 42.
Wang, K., Li, M., & Hakonarson, H.
(2010). ANNOVAR: functional annotation of genetic variants from
high-throughput sequencing data. Nucleic acids research, 38 (16),
e164-e164.
Goldstein, J. I., Crenshaw, A., Carey, J., Grant, G. B., Maguire, J.,
Fromer, M., … Neale, B. M. (2012). zCall: a rare variant caller
for array-based genotyping: genetics and population analysis.
Bioinformatics (Oxford, England), 28(19), 2543–2545.
doi:10.1093/bioinformatics/bts479