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Mahadevan L.,Medgenome Labs | Yesudas A.,Medgenome Labs | Sajesh P.K.,Medgenome Labs | Revu S.,Medgenome Labs | And 7 more authors.
Indian Journal of Human Genetics | Year: 2014

BACKGROUND AND AIM: This study reports the prevalence of five clinically significant variants associated with increased risk of cardiovascular disorders, and variable responses of individuals to commonly prescribed cardiovascular drugs in a South Indian population from the state of Kerala.MATERIALS AND METHODS: Genomic DNA isolated from 100 out-patient samples from Kerala were sequenced to examine the frequency of clinically relevant polymorphisms in the genes MYBPC3 (cardiomyopathy), SLCO1B1 (statin-induced myopathy), CYP2C9, VKORC1 (response to warfarin) and CYP2C19 (response to clopidogrel).RESULTS: Our analyses revealed the frequency of a 25 bp deletion variant of MYBPC3 associated with risk of cardiomyopathy was 7%, and the SLCO1B1 "C" allele associated with risk for statin-induced myopathy was 15% in this sample group. Among the other variants associated with dose-induced toxicity of warfarin, VKORC1 (c.1639G>A), was detected at 22%, while CYP2C9∗3 and CYP2C9∗2 alleles were present at a frequency of 15% and 3% respectively. Significantly, the tested sample population showed high prevalence (66%) of CYP2C19∗2 variant, which determines response to clopidogrel therapy.CONCLUSIONS: We have identified that certain variants associated with cardiovascular disease and related drug response in the five genes, especially those in VKORC1, CYP2C19 and MYBPC3, are highly prevalent in the Kerala population, with almost 2 times higher prevalence of CYP2C19∗2 variant compared with other regions in the country. Since the variants chosen in this study have relevance in disease phenotype and/or drug response, and are detected at a higher frequency, this study is likely to encourage clinicians to perform genetic testing before prescribing therapy.


Aggarwal S.,Nizam's Institute of Medical Sciences | Aggarwal S.,DNA Diagnostics Center | Bhowmik A.D.,DNA Diagnostics Center | Ramprasad V.L.,Medgenome Labs | And 2 more authors.
American Journal of Medical Genetics, Part A | Year: 2016

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. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.


Rajendran S.,Research Center | Sundaresan L.,Research Center | Rajendran K.,Research Center | Selvaraj M.,Research Center | And 4 more authors.
Biorheology | Year: 2016

Background: Fluid flow plays an important role in vascular development. However, the detailed mechanisms, particularly the link between flow and modulation of gene expression during vascular development, remain unexplored. In chick embryo, the key events of vascular development from initiation of heart beat to establishment of effective blood flow occur between the stages HH10 and HH13. Therefore, we propose a novel in vivo model to study the flow experienced by developing endothelium. Objective: Using this model, we aimed to capture the transcriptome dynamics of the pre- and post-flow conditions. Methods: RNA was isolated from extra embryonic area vasculosa (EE-AV) pooled from three chick embryos between HH10-HH13 and RNA sequencing was performed. Results: The whole transcriptome sequencing of chick identified up-regulation of some of the previously well-known mechanosensitive genes including NFR2, HAND1, CTGF and KDR. GO analyses of the up-regulated genes revealed enrichment of several biological processes including heart development, extracellular matrix organization, cell-matrix adhesion, cell migration, blood vessel development, patterning of blood vessels, collagen fibril organization. Genes encoding for gap junctions proteins which are involved in vascular remodeling and arterial-venous differentiation, and genes involved in cell-cell adhesion, and ECM interactions were significantly up-regulated. Validation of selected genes through semi quantitative PCR was performed. Conclusion: The study indicates that shear stress plays a major role in development. Through appropriate validation, this platform can serve as an in vivo model to study conditions of disturbed flow in pathology as well as normal flow during development. © 2016 - IOS Press and the authors. All rights reserved.


Adduri R.S.R.,DNA Diagnostics Center | Katamoni R.,DNA Diagnostics Center | Katamoni R.,French National Center for Scientific Research | Pandilla R.,DNA Diagnostics Center | And 5 more authors.
PLoS ONE | Year: 2014

Purpose: The tumor suppressor p53 is known to be inactivated frequently in various cancers. In addition, germline polymorphisms in TP53 are known to affect protein function and influence risk of developing different types of cancers. In this study, we analyzed the association of TP53 Pro72Arg polymorphism with squamous cell carcinoma of oral tongue (SCCOT) and esophagus (ESCC) in India. Methods: We assessed the distribution of TP53 Pro72Arg polymorphism in one hundred and fifteen and eighty two SCCOT and ESCC patients, respectively, with respect to one hundred and ten healthy controls from the same population. In addition, we analyzed association of the polymorphism with several clinicopathological and molecular parameters. Results: Pro72 allele was significantly enriched in SCCOT patients compared to the healthy control group but neither allele was enriched in ESCC. Interestingly, Pro72 allele was preferentially mutated in ESCC which was confirmed by analysis of samples heterozygous for Pro72Arg. Conclusions: Our study revealed the association of Pro72 allele with SCCOT suggesting the effect of this polymorphism on SCCOT risk. Preferential mutation of Pro72 allele exclusively in ESCC indicates the need for further studies to understand the tissue specific effect of p53 polymorphism. © 2014 Adduri et al.


PubMed | Nizam's Institute of Medical Sciences, DNA Diagnostics Center and Medgenome Labs
Type: Journal Article | Journal: American journal of medical genetics. Part A | Year: 2016

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. 2016 Wiley Periodicals, Inc.


Medgenome Labs | Entity website

MGM070 Lymphoproliferative disorder gene panel NGS 6 WEEKS Bone marrow / tissue / EDTA blood / DNA MGM167 Lynch Syndrome 4 gene (MLH1,MLH2, MSH6 & PMS2) panel NGS 4 WEEKS Peripheral Blood / Purified Genomic DNA MGM168 ALL risk stratification gene panel B-ALL NGS 3 WEEKS Peripheral Blood / Bone Marrow / Purified Genomic DNA MGM169 ALL risk stratification gene panel T-ALL NGS 3 WEEKS Peripheral Blood / Bone Marrow / Purified Genomic DNA MGM170 AML risk stratification gene panel NGS 3 WEEKS Peripheral Blood / Bone Marrow / Purified Genomic DNA MGM171 APC gene analysis NGS 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM172 APC gene analysis Sanger 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM173 BCR-ABL qualitative gene fusion analysis Qualitative RT-PCR+ 5 DAYS Peripheral Blood MGM174 BCR-ABL quantitative (International Scale) gene fusion analysis RT-PCR+ 7 DAYS Peripheral Blood MGM175 BCR-ABL quantitative gene fusion analysis RT-PCR+ 7 DAYS Peripheral Blood MGM176 BRAF gene analysis 2 exons (11 & 15) Sanger+ 7 DAYS Fresh frozen tissue/FFPE blocks/Glass slides MGM177 BRAF V600E mutation analysis RT-PCR 7 DAYS Fresh frozen tissue/FFPE blocks/Glass slides MGM178 BRCA1 & BRCA2 deletion/duplication analysis MLPA 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM179 BRCA1 & BRCA2 gene analysis NGS 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM180 BRCA1 & BRCA2 gene analysis Sanger+ 6 WEEKS Peripheral Blood / Purified Genomic DNA MGM181 BRCA1 gene analysis Sanger+ 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM182 BRCA2 gene analysis Sanger+ 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM183 Carney complex (PRKAR1A) gene analysis NGS 4 WEEKS Peripheral Blood / Purified Genomic DNA MGM184 Chronic myeloproliferative disorder gene panel (CMPD) NGS 3 WEEKS Peripheral Blood / Bone Marrow/ Purified Genomic DNA MGM185 CLL prognostication/risk stratification gene panel NGS 3 WEEKS Peripheral Blood / Bone Marrow/ Purified Genomic DNA MGM186 CML/CNL (atypical) prognostication gene panel NGS 3 WEEKS Peripheral Blood / Bone Marrow/ Purified Genomic DNA MGM187 Comprehensive cancer gene panel (germline) NGS 6 WEEKS Peripheral Blood / Purified Genomic DNA MGM188 EFT/PNET Fusion Transcript Analysis RT-PCR 10 DAYS Fresh frozen tissue/FFPE blocks/Glass slides MGM189 EGFR gene analysis 4 exons (18, 19, 20, 21) Sanger+ 10 DAYS Fresh frozen tissue/FFPE blocks MGM190 EGFR gene analysis (Hot Spot) RT-PCR+ 7 DAYS Fresh frozen tissue/FFPE blocks MGM191 Familial MDS-AML gene panel NGS 3 WEEKS Peripheral Blood / Bone Marrow/ Purified Genomic DNA MGM192 Familial MDS-AML gene panel-reflex MLPA 3 WEEKS Peripheral Blood / Bone Marrow/ Purified Genomic DNA MGM193 FLT3 gene internal tandem duplication analysis and D835 point mutation analysis Fragment analysis & Sanger 2 WEEKS Bone Marrow/ Purified Genomic DNA MGM194 Hereditary cancer gene panel NGS 6 WEEKS Peripheral Blood / Purified Genomic DNA MGM195 HNPCC gene panel NGS 4 WEEKS Peripheral Blood / Purified Genomic DNA MGM196 Somatic cancer mutation Hot spot tumor panel NGS 4 WEEKS Fresh frozen tissue/FFPE blocks & Peripheral Blood in 2 Streck Tubes MGM197 IDH1 gene analysis Sanger+ 7 DAYS Peripheral Blood; Fresh frozen tissue/FFPE blocks MGM198 Imatinib Resistance (ABL kinase) gene analysis Sanger+ 10 DAYS Peripheral Blood MGM199 JAK2 gene analysis 2 exons (12, 14) Sanger+ 7 DAYS Peripheral Blood / Bone Marrow/ Purified Genomic DNA MGM200 JMML risk stratification gene panel NGS 3 WEEKS Peripheral Blood / Bone Marrow/ Purified Genomic DNA MGM201 KIT gene analysis 2 exons (9,11) Sanger+ 7 DAYS Fresh frozen tissue/FFPE blocks MGM202 KIT gene analysis 4 exons (9, 11, 13, 17) Sanger+ 10 DAYS Fresh frozen tissue/FFPE blocks MGM203 KRAS gene analysis (Hot Spot) NGS 7 DAYS Fresh frozen tissue/FFPE blocks MGM204 KRAS gene analysis 2 exons (2 & 3) Sanger+ 7 DAYS Fresh frozen tissue/FFPE blocks MGM205 LCH/hairy cell leukemia BRAF V600E mutation analysis NGS 3 WEEKS Peripheral Blood / Bone Marrow MGM206 MDS prognostication and risk stratification gene panel NGS 3 WEEKS Peripheral Blood / Bone Marrow MGM207 MGMT gene methylation analysis RT-PCR 2 WEEKS Fresh frozen tissue/FFPE blocks MGM208 MPN CALR (exon 9) gene analysis Fragment analysis 7 DAYS Peripheral Blood / Bone Marrow MGM209 MPN JAK2 V617F mutation analysis Sanger+ 7 DAYS Peripheral Blood / Bone Marrow MGM210 MPN MPL (exon 10) gene analysis Sanger 7 DAYS Peripheral Blood / Bone Marrow MGM211 MPN prognostication and risk stratification gene panel NGS 3 WEEKS Peripheral Blood / Bone Marrow MGM212 NF1 deletion/duplication analysis MLPA+ 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM213 NF1 gene sequencing NGS 4 WEEKS Peripheral Blood / Purified Genomic DNA MGM214 NF2 deletion/duplication analysis MLPA+ 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM215 NF2 gene sequencing NGS 4 WEEKS Peripheral Blood / Purified Genomic DNA MGM216 NPM1 gene analysis (Hot Spot exon 12) Fragment analysis 2 WEEKS Peripheral Blood / Bone Marrow MGM217 NRAS gene analysis (Hot Spot) RT-PCR 7 DAYS Fresh frozen tissue / FFPE blocks MGM218 PDGFRA gene analysis 3 exons (12, 14, 18) Sanger+ 10 DAYS Peripheral blood/Bone marrow/Fresh frozen tissue / FFPE blocks MGM219 PML-RARa gene fusion analysis Qualitative RT-PCR+ 10 DAYS Peripheral Blood / Bone Marrow MGM220 PTEN gene analysis Sanger 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM221 RB1 gene analysis NGS 4 WEEKS Peripheral Blood / Purified Genomic DNA MGM222 RB1 gene deletion/duplication analysis MLPA+ 3WEEKS Peripheral Blood / Purified Genomic DNA MGM223 RET oncogene 2 exons (10, 11) Sanger+ 10 DAYS Peripheral Blood / Purified Genomic DNA MGM224 RET oncogene 8 exons (5, 8, 10, 11, 13, 14, 15, 16) Sanger+ 6 WEEKS Peripheral Blood / Purified Genomic DNA MGM225 ROS1 gene fusion analysis RT-PCR 2 WEEKS Fresh frozen tissue / FFPE blocks MGM226 STK11 gene analysis Sanger 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM227 TP53 gene analysis NGS 4 WEEKS Peripheral Blood / Purified Genomic DNA MGM228 TP53 gene analysis Sanger+ 3 WEEKS Peripheral Blood / Purified Genomic DNA MGM235 VHL gene analysis Sanger+ 10 DAYS Peripheral Blood / Purified Genomic DNA IMMUNOHISTOCHEMISTRY MGM236 ALK D5F3 IHC 4 DAYS Fresh frozen tissue/FFPE blocks MGM237 BRAF V600E IHC analysis IHC 4 DAYS Fresh frozen tissue/FFPE blocks blocks MGM238 c-MET IHC analysis IHC 4 DAYS Fresh frozen tissue/FFPE blocks MGM239 Prognostic/predictive IHC1 panel (ANY ONE OF ER, PR, Her2/neu, MIB-1/Ki67) IHC 4 DAYS Fresh frozen tissue/FFPE blocks MGM240 Prognostic/predictive IHC2 panel (ER, PR): IHC 4 DAYS Fresh frozen tissue/FFPE blocks MGM241 Prognostic/predictive IHC3 panel (ER, PR, Her2/neu): IHC 4 DAYS Fresh frozen tissue/FFPE blocks MGM242 Prognostic/predictive IHC4 panel (ER, PR, Her2/neu, MIB-1/Ki67) IHC 4 DAYS Fresh frozen tissue/FFPE blocks MGM243 ROS1 IHC analysis IHC 4 DAYS Fresh frozen tissue/FFPE blocks


PubMed | St Thomas Hospital, Medgenome Labs and Karpagam University
Type: Journal Article | Journal: Indian journal of human genetics | Year: 2014

This study reports the prevalence of five clinically significant variants associated with increased risk of cardiovascular disorders, and variable responses of individuals to commonly prescribed cardiovascular drugs in a South Indian population from the state of Kerala.Genomic DNA isolated from 100 out-patient samples from Kerala were sequenced to examine the frequency of clinically relevant polymorphisms in the genes MYBPC3 (cardiomyopathy), SLCO1B1 (statin-induced myopathy), CYP2C9, VKORC1 (response to warfarin) and CYP2C19 (response to clopidogrel).Our analyses revealed the frequency of a 25 bp deletion variant of MYBPC3 associated with risk of cardiomyopathy was 7%, and the SLCO1B1 C allele associated with risk for statin-induced myopathy was 15% in this sample group. Among the other variants associated with dose-induced toxicity of warfarin, VKORC1 (c.1639G>A), was detected at 22%, while CYP2C9*3 and CYP2C9*2 alleles were present at a frequency of 15% and 3% respectively. Significantly, the tested sample population showed high prevalence (66%) of CYP2C19*2 variant, which determines response to clopidogrel therapy.We have identified that certain variants associated with cardiovascular disease and related drug response in the five genes, especially those in VKORC1, CYP2C19 and MYBPC3, are highly prevalent in the Kerala population, with almost 2 times higher prevalence of CYP2C19*2 variant compared with other regions in the country. Since the variants chosen in this study have relevance in disease phenotype and/or drug response, and are detected at a higher frequency, this study is likely to encourage clinicians to perform genetic testing before prescribing therapy.


PubMed | Medgenome Labs, Singapore Eye Research Institute, Narayana Nethralaya, GROW Research Laboratory and Strand Life science Pvt. Ltd.
Type: | Journal: BioMed research international | Year: 2015

Stargardt disease (STGD) is the leading cause of juvenile macular degeneration associated with progressive central vision loss, photophobia, and colour vision abnormalities. In this study, we have described the clinical and genetic features of Stargardt patients from an Indian cohort. The next generation sequencing was carried out in five clinically confirmed unrelated patients and their family members using a gene panel comprising 184 retinal specific genes. Sequencing results were analyzed by read mapping and variant calling in genes of interest, followed by their verification and interpretation. Genetic analysis revealed ABCA4 mutations in all of the five unrelated patients. Among these, four patients were found with compound heterozygous mutations and another one had homozygous mutation. All the affected individuals showed signs and symptoms consistent with the disease phenotype. We report two novel ABCA4 mutations in Indian patients with STGD disease, which expands the existing spectrum of disease-causing variants and the understanding of phenotypic and genotypic correlations. Screening for causative mutations in patients with STGD using panel of targeted gene sequencing by NGS would be a cost effective tool, might be helpful in confirming the precise diagnosis, and contributes towards the genetic counselling of asymptomatic carriers and isolated patients.


News Article | April 21, 2014
Site: www.biospectrumasia.com

Mr Sam Santhosh, the founder of MedGenome has been an entrepreneur, with over 20 years' of experience in the software industry. Currently, he is also the CEO and chairman of SciGenom Labs. SciGenom is a genomics company, also based in Cochin and founded by Mr Santhosh, which explores and exploits the advances in genomic technologies to bring new services and products to the lifesciences industry. Prior to this, Mr Santhosh was the CEO and MD of California Software Limited (Calsoft) from 1992-2012. "The completion of the first draft of the Human Genome and the explosive growth of sequencing technologies attracted him to start SciGenom and MedGenome," says Dr V L Ramprasad, COO and principal scientist, MedGenome Labs. The services MedGenome provides molecular genetic diagnostics using Sanger Sequencing and Next Generation Sequencing (NGS) technologies for personalized healthcare. "The major services offered by SciGenom are Next Generation Sequencing and software tools around it. The human genetic testing (diagnostic) services have been incubated as a separate entity, which is MedGenome," adds Dr Ramprasad. "Molecular diagnostic tests can help determine which variations in the patient's genes should be targeted for the right treatment option, especially in cancer," explains Dr Ramprasad. He goes on, saying, "The tests will aid clinicians in screening to help predict the risk of developing a specific disease. We also develop software tools that help clinicians demystify genomic data so that they can take appropriate clinical decisions. Apart from the genetic tests that are targeted at the one gene and one disease level, we can do whole exome sequencing and whole genome sequencing. This can sequence hundreds of genes and MedGenome's expertise is in picking the needle in a haystack." The company aims to start molecular tests that will do away with invasive methods like tissue biopsies in cancer patients and amniocentesis in pregnant women soon. "The main challenge was in getting the medical market to understand the value of genetic tests. Secondly, developing low-cost tests and a strong bioinformatics team was the next challenge. The current high customs duty on raw materials still remains a challenge," voiced Dr Ramprasad. Funding and setbacks Initially, Mr Sam Santhosh was the sole investor while establishing the company. "Now MedGenome has raised $5 million through Emerge Ventures, a venture capital company based in Singapore," he adds. Currently, the company caters to academic translational research centers, tertiary hospitals, specialty clinics, oncologists and pharma companies. "Being incubated at SciGenom," he says, "we did not have to face serious issues like other start-ups. The main challenge was getting the right people with the requisite skills." For young entrepreneurs who want to set foot in the start-up circle, Dr Ramprasad advises, "Any start-up needs to ensure that its services and products meet customers' needs by providing real value. Then, you need to ensure that the company has sufficient funding and a well-qualified management team." Expansion strategy Talking about MedGenome's expansion plans, Dr Ramprasad adds, "We are buoyed by the positive response that we are getting from the industry and market for our service offerings. We are allocating additional resources to scale up the operations. We are starting a state-of-the-art lab in Bangalore which will soon become the hub of MedGenome operations." MedGenome also plans to start satellite labs across the country to expand its services. "The bioinformatics tools and services that we are developing are going to be the key for our success," he said.

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