Publications

At MedGenome, we are deeply focused on continuous innovation, and publishing our findings for the larger benefit of the genetic testing community. Read through our publications for details of our latest work.
Optimization and Validation of a Harmonized Protocol for Generating Therapeutic-Grade Dendritic Cells in a Randomized Phase II Clinical Trial, Using Two Varied Antigenic Sources.

Journal: Vaccines (Basel) | January 2024

Author: Abirami Seetharaman, Vasanth Christopher, Hemavathi Dhandapani, Hascitha Jayakumar, Manikandan Dhanushkodi, Narmadha Bhaskaran, Swaminathan Rajaraman, Rama Ranganathan, Shirley Sunder Singh, Varalakshmi Vijayakumar, Arivazhagan Rajamanickam, Anil Suri, Nirmala Jagadish, Thangarajan Rajkumar and Priya Ramanathan Abirami Seetharaman, Vasanth Christopher, Hemavathi Dhandapani, Hascitha Jayakumar, Manikandan Dhanushkodi, Narmadha Bhaskaran, Swaminathan Rajaraman, Rama Ranganathan, Shirley Sunder Singh, Varalakshmi Vijayakumar, Arivazhagan Rajamanickam, Anil Suri, Nirmala Jagadish, Thangarajan Rajkumar and Priya Ramanathan

Abstract:

Autologous dendritic cell (DC)-based immunotherapy is a cell-based advanced therapy medicinal product (ATMP) that was first introduced more than three decades ago. In the current study, our objective was to establish a harmonized protocol using two varied antigenic sources and a good manufacturing practice (GMP)-compliant, manual method for generating clinical-grade DCs at a limited-resource academic setting. After obtaining ethical committee-approved…

Acute lymphoblastic leukemia with myeloid mutations is a high-risk disease associated with clonal hematopoiesis

Journal: Blood Cancer Discovery | December 2023

Author: Caner Saygin, Pu Zhang, Jacob Stauber, Ibrahim Aldoss, Adam S Sperling, Lachelle D Weeks, Marlise R Luskin, Todd C Knepper, Pankhuri Wanjari, Peng Wang, Angela M Lager, Carrie Fitzpatrick, Jeremy P Segal, Mehdi Gharghabi, Sandeep Gurbuxani, Girish Venkataraman, Jason X Cheng, Bart J Eisfelder, Oliver Bohorquez, Anand A Patel, Sheethal Umesh Nagalakshmi, Savita Jayaram, Olatoyosi M Odenike, Richard A Larson, Lucy A Godley, Daniel A Arber, Christopher J Gibson, Nikhil C Munshi, Guido Marcucci, Benjamin L Ebert, John M Greally, Ulrich Steidl, Rosa Lapalombella, Bijal D Shah and Wendy Stoc

Abstract:

Myeloid neoplasms arise from pre-existing clonal hematopoiesis (CH), however the role of CH in pathogenesis of ALL is unknown. We found that 18% of adult ALL cases harbored TP53, and 16% had myeloid CH-associated gene mutations. ALL with myeloid mutations (MyM) had distinct genetic and clinical characteristics, associated with inferior survival. By using single cell proteogenomic analysis, we demonstrated that…

Diagnostic exome identifies a novel PRKG2 mutation in a proband with skeletal dysplasia

Journal: Clinical Genetics | December 2023

Author: Payal Kamdar, Thenral S. Geetha, Thomas Palocaren, Madhavi Kandagaddala, Praveen Kumar Chinniah, Sakthivel Murugan, Ramprasad Vedam, Sumita Danda

Abstract:

This graphic abstract combines pedigree, dysmorphology features, radiographs, and the PRKG2 protein domain, specifically the CNB-A regulatory domain, which harbors a mutation resulting in premature protein termination.

The Genetic Drivers Of Juvenile, Young, And Early-Onset Parkinson’s Disease In India

Journal: Movementdisorders | November 2023

Author: Shan V. Andrews PhD, Prashanth L. Kukkle DM, Ramesh Menon PhD, Thenral S. Geetha PhD, Vinay Goyal DM, Rukmini Mridula Kandadai DM, Hrishikesh Kumar DM, Rupam Borgohain DM, Adreesh Mukherjee DM, Pettarusp M. Wadia DM, Ravi Yadav DM, Soaham Desai DM, Niraj Kumar DM, Deepika Joshi DM, Sakthivel Murugan PhD, Atanu Biswas DM, Pramod K. Pal DM, Merina Oliver MSc, Sandhya Nair PhD, Anbu Kayalvizhi MSc, Praveena L. Samson MSc, Manjari Deshmukh MSc, Akshi Bassi MTech, Charugulla Sandeep MTech, Nitin Mandloi MSc, Oliver B. Davis PhD, Melissa A. Roberts PhD, Dara E. Leto PhD, Anastasia G. Henry PhD, Gilbert Di Paolo PhD, Uday Muthane DM, Shymal K. Das DM, Andrew S. Peterson PhD, Thomas Sandmann PhD, Ravi Gupta PhD, Vedam L. Ramprasad PhD, Parkinson Research Alliance Of India (PRAI)

Abstract:

Recent studies have advanced our understanding of the genetic drivers of Parkinson’s disease (PD). Rare variants in more than 20 genes are considered causal for PD, and the latest PD genome-wide association study (GWAS) identified 90 independent risk loci. However, there remains a gap in our understanding of PD genetics outside of the European populations in which the vast majority…

Clinical Utility of Proband Only Clinical Exome Sequencing in Neurodevelopmental Disorders

Journal: Indian Journal of Pediatrics | November 2023

Author: Karthika Ajit Valaparambil, Alfiya Fasaludeen, Lakshmi Priya, Ramshekhar N. Menon, Ramesh Menon & Soumya Sundaram

Abstract:

Chromosomal microarray is recommended as the first line of investigation in neurodevelopmental disorders (NDDs). However, advances in next-generation sequencing have unraveled more than 900 genes associated with NDDs, thus improving the genetic diagnosis. Therefore, this study was conducted to explore the utility of clinical exome sequencing (CES) in NDDs from a tertiary care centre in India. A retrospective observational analysis…

Kindler syndrome with a novel mutation and a rare gynaecological complication

Journal: Clinical and Experimental Dermatology | October 2023

Author: Pavithren Tanigassalame, Aravind Baskar Murthy, Vijayasankar Palaniappan, Kaliaperumal Karthikeyan, T Senthil Kumar

Abstract:

Kindler syndrome is a rare genodermatosis characterized by mechanical skin fragility, acral blisters, photosensitivity, poikiloderma, skin atrophy and mucosal inflammation.1 It is considered a subtype of inherited epidermolysis bullosa. The disease is inherited in an autosomal recessive pattern with the parents of the affected individuals being obligate heterozygotes.2 We report a case of a patient with Kinder syndrome with a giant myometrial…

Identification of a shared, common haplotype segregating with an SGCB c.544 T > G mutation in Indian patients affected with sarcoglycanopathy

Journal: Nature Scientific reports | September 2023

Author: Shamita Sanga, Sudipta Chakraborty, Mainak Bardhan, Kiran Polavarapu, Veeramani Preethish Kumar, Chandrika Bhattacharya, Saraswati Nashi, Seena Vengalil, Thenral S Geetha, Vedam Ramprasad, Atchayaram Nalini, Analabha Basu, Moulinath Acharya

Abstract:

Sarcoglycanopathy is the most frequent form of autosomal recessive limb-girdle muscular dystrophies caused by mutations in SGCB gene encoding beta-sarcoglycan proteins. In this study, we describe a shared, common haplotype co-segregating in 14 sarcoglycanopathy cases from 13 unrelated families from south Indian region with the likely pathogenic homozygous mutation c.544 T > G (p.Thr182Pro) in SGCB.

Detection of 22q11.2 deletion syndrome by single-nucleotide polymorphism based non-invasive prenatal test

Journal: Indian Journal of Obstetrics and Gynecology Research | August 2023

Author: Angela Devanboo, Dhriti Chendil Nathan, Shweta Kannan Mahalingam, Vishalakshi Apparaya Prabhu, Hema Purandarey, E Venkataswamy, V. L. Ramprasad, Priya Kadam

Abstract:

Non-invasive prenatal test (NIPT) has become a popular screening test worldwide for screening common trisomies. In addition, the test can also sex chromosomal aneuploidies (SCAs) with similar sensitivity. In recent years, the scope of NIPT has extended to screen pregnancies for clinically significant microdeletions (MDs), rare autosomal aneuploidies, and subchromosomal abnormalities.

South Asian medical cohorts reveal strong founder effects and high rates of homozygosity

Journal: Nature Communication | August 2023

Author: Jeffrey D. Wall, J. Fah Sathirapongsasuti, Ravi Gupta, Asif Rasheed, Radha Venkatesan, Saurabh Belsare, Ramesh Menon, Sameer Phalke, Anuradha Mittal, John Fang, Deepak Tanneeru, Manjari Deshmukh, Akshi Bassi, Jacqueline Robinson, Ruchi Chaudhary, Sakthivel Murugan, Zameer ul-Asar, Imran Saleem, Unzila Ishtiaq, Areej Fatima, Saqib Shafi Sheikh, Shahid Hameed, Mohammad Ishaq, Syed Zahed Rasheed, Andrew S. Peterson

Abstract:

The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927…

Genotype-phenotype correlation and natural history study of dysferlinopathy: a single-centre experience from India

Journal: Neurogenetics | December 2022

Author: Saraswati Nashi, Kiran Polavarapu, Mainak Bardhan, Ram Murthy Anjanappa, Veeramani Preethish-Kumar, Seena Vengalil, Hansashree Padmanabha, Thenral S Geetha, P V Prathyusha, Vedam Ramprasad, Aditi Joshi, Tanushree Chawla, Gopikirshnan Unnikrishnan, Pooja Sharma, Akshata Huddar, Bharathram Uppilli, Abel Thomas, Dipti Baskar, Susi Mathew, Deepak Menon, Gautham Arunachal, Mohammed Faruq, Kumarasamy Thangaraj, Atchayaram Nalini

Abstract:

Dysferlinopathies are a group of limb-girdle muscular dystrophies causing significant disability in the young population. There is a need for studies on large cohorts to describe the clinical, genotypic and natural history in our subcontinent. To describe and correlate the clinical, genetic profile and natural history of genetically confirmed dysferlinopathies.

Exome sequencing and microarray identified a novel large exonic deletion in SYT2 gene in an ultra-rare case with recessive CMS type 7.

Journal: J Genet | December 2022

Author: Mukesh Desai, Thenral S Geetha, Vedam Ramprasad, Ritu Kashikar.

Abstract:

Congenital myasthenic syndromes (CMSs) are a diverse group of diseases that have an underlying defect in transmission of signals from nerve cells to muscles that lead to muscular weakness. A 13-year-old male child born of consanguineous parents with profound motor developmental delay and normal cognition was referred to us.

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation

Journal: Giga Science | December 2022

Author: Harsh Shukla, Kushal Suryamohan, Anubhab Khan, Krishna Mohan, Rajadurai C Perumal, Oommen K Mathew, Ramesh Menon, Mandumpala Davis Dixon, Megha Muraleedharan, Boney Kuriakose, Saju Michael, Sajesh P Krishnankutty, Arun Zachariah, Somasekar Seshagiri, Uma Ramakrishnan

Abstract:

The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management.

A novel compound heterozygous BEST1 gene mutation in two siblings causing autosomal recessive bestrophinopathy

Journal: BMC ophthalmology | December 2022

Author: Obaid Imtiyazul Haque, Anbukayalvizhi Chandrasekaran, Faisal Nabi, Owais Ahmad, João Pedro Marques, Tanweer Ahmad

Abstract:

To describe the clinical features, imaging characteristics, and genetic test results associated with a novel compound heterozygous mutation of the BEST1 gene in two siblings with autosomal recessive bestrophinopathy. Methods Two siblings underwent a complete ophthalmic examination, including dilated fundus

Prenatal Diagnosis for Primary Immunodeficiency Disorders-An Overview of the Indian Scenario

Journal: Frontiers in immunology | December 2022

Author: Reetika Malik Yadav, Maya Gupta, Aparna Dalvi, Umair Ahmed Bargir, Gouri Hule, Snehal Shabrish, Jahnavi Aluri, Manasi Kulkarni, Priyanka Kambli, Ramya Uppuluri, Suresh Seshadri, Sujatha Jagadeesh, Beena Suresh, Jayarekha Raja, Prasad Taur, Sivasankar Malaischamy, Priyanka Ghosh, Shweta Mahalingam, Priya Kadam, Harsha Prasada Lashkari, Parag Tamhankar, Vasundhara Tamhankar, Shilpa Mithbawkar, Sagar Bhattad, Prerna Jhawar, Adinarayan Makam, Vandana Bansal, Malathi Prasad, Geeta Govindaraj, Beena Guhan, Karthik Bharadwaj Tallapaka, Mukesh Desai, Revathi Raj, Manisha Rajan Madkaikar

Abstract:

Prenatal Diagnosis (PND) forms an important part of primary preventive management for families having a child affected with primary immunodeficiency. Although individually sparse, collectively this group of genetic disorders represents a significant burden of disease. This paper discusses the prenatal services available for affected families at various centers across the country and the challenges and ethical considerations associated with genetic…

Clinico-epidemiological and genomic profile of first Zika Virus outbreak in India at Jaipur city of Rajasthan state

Journal: Journal of infection and public health | December 2022

Author: Bharti Malhotra, Veenu Gupta, Pratibha Sharma, Ruchi Singh, Himanshu Sharma, Madhavi Vyas, Ravi P Mathur, Virender K Mathur, Deepa Meena, Hemant Malhotra, Pragya D Yadav, Gajanan Sapkal, Ullas Pt, Gururaj Rao Deshpande, Rashmi Gunjikar, Heena Shaman, Devendra T Mourya, Nivedita Gupta, Sujit Singh, P Ravindran, Jitender Tiwari, Dimpal A Nyayanit, Neeraj Kumar, Sameer Phalke, Anup Chugani, Sudhir Bhandari, Prashanth Suravajhala, Pooran Singh Solanki, Manila Salaria

Abstract:

First Zika virus (ZIKV) positive case from North India was detected on routine surveillance of Dengue-Like Illness in an 85-year old female. Objective of the study was to conduct an investigation for epidemiological, clinical and genomic analysis of first ZIKV outbreak in Rajasthan, North India and enhance routine ZIKV surveillance.

Think of SCA45 in Late-Onset Familial Ataxias: The First Report from the Indian Subcontinent with a Novel Variant

Journal: Movement disorders clinical practice | October 2022

Author: Jacky Ganguly 1, Soumava Mukherjee 2, Purba Basu 1, Banashree Mondal 1, Koustav Chatterjee 1, Akash Roy 1, Priyadarshini Pande 3, Hrishikesh Kumar 1

Abstract:

An 82-year-old male patient presented with insidious onset and slowly progressive imbalance during walking over a period of the last 20 years. He also suffered from recurrent bouts of bullous pemphigoid for the last 30 years and developed hearing difficulty for the last 3 years. He had a strong family history of late onset gait imbalance involving his mother, four of his elder…

Multiomic analysis of papillary thyroid cancers identifies BAIAP2L1-BRAF fusion and requirement of TRIM25, PDE5A and PKCδ for tumorigenesis

Journal: Molecular cancer | October 2022

Author: Emilie Renaud 1, Kristina Riegel 1, Rossana Romero 1, Kushal Suryamohan 2, Ute Distler 3, Stefan Tenzer 3, Arno Schad 4, Thomas J Musholt 5, Krishnaraj Rajalingam 6

Abstract:

Papillary thyroid carcinoma (PTC) is one of the most common forms of thyroid cancer with a cure rate of over 90% after surgery. However, aggressive forms may still occur, and personalized therapeutic strategies are increasingly required. Methods We performed integrated genomic and proteomic analysis of PTC tumor samples from patients who did not harbor BRAF or RAS mutations.

Galectin antagonist use in mild cases of SARS-CoV-2; pilot feasibility randomised, open label, controlled trial

Journal: MedRxiv | December 2021

Author: Alben Sigamani, Samarth Shetty, Madhavi, Mathu Ruthra, Sudhishma, Anup Chugani, Hana Chen-Walden, ThomasKutty, David Platt

Abstract:

Importance Novel SARS-CoV-2 virus has infected nearly half a billion people across the world and is highly contagious. There is a need for a novel mechanism to block viral entry and stop its replication. Background Spike protein N terminal domain (NTD) of the novel SARS-CoV-2 is essential for viral entry and replication in human cell.

Maternal opioid use disorder: Placental transcriptome analysis for neonatal opioid withdrawal syndrome

Journal: Genomics | November 2021

Author: Uppala Radhakrishna 1, Swapan K Nath 2, Sangeetha Vishweswaraiah 3, Lavanya V Uppala 4, Ariadna Forray 5, Srinivas B Muvvala 5, Nitish K Mishra 6, Siddesh Southekal 6, Chittibabu Guda 6, Hiranjith Govindamangalam 7, Derek Vargas 7, William G Gardella 3, Richard C Crist 8, Wade H Berrettini 9, Raghu P Metpally 10, Ray O Bahado-Singh 3

Abstract:

Excessive prenatal opioid exposure may lead to the development of Neonatal Opioid Withdrawal Syndrome (NOWS). RNA-seq was done on 64 formalin-fixed paraffin-embedded placental tissue samples from 32 mothers with opioid use disorder, with newborns with NOWS that required treatment, and 32 prenatally unexposed controls. We identified 93 differentially expressed genes in the placentas of infants with NOWS compared to unexposed…

Novel Consensus Splice Site Pathogenic Variation in THOC2 Gene Leads to Recurrent Arthrogryposis Multiplex Congenita Phenotype: A Case Report

Journal: Cureus | November 2021

Author: Vasundhara Tamhankar, Parag Tamhankar, Rajas Chaubal, Jyoti Chaubal, Nitin Chaubal

Abstract:

The THOC2 gene encodes THO complex subunit 2, a subunit of the Transcription-Export (TREX) complex which binds specifically to splice messenger ribonucleic acid (mRNAs) to facilitate mRNA export. Mutations in the THOC2 gene have been described to lead to X-linked mental retardation syndrome type 12/35 (XLMR-12/35) (MIM#300957).

Drug-resistant ‘Non-Lesional’ Visual Sensitive Epilepsies of Childhood – Electroclinical Phenotype-Genotype Associations

Journal: Neurology India | November 2021

Author: Ramshekhar N Menon 1, Poornima N Nambiar 1, R Ravish Keni 1, Jitupam Baishya 1, Ashalatha Radhakrishnan 1, Ajith Cherian 1, Sheela Nampoothiri 2, G K Madhavilatha 3, Udaya H Kotecha 3, Sanjeev V Thomas 1

Abstract:

Sporadic nonlesional intractable visual-sensitive epilepsies of childhood represent a challenging subset of epilepsies in terms of management and prognostication given a propensity to evolve as epileptic encephalopathy. Objective: To study the genetic heterogeneity of drug-resistant visual sensitive epilepsy of childhood.

NGS-Based Expanded Carrier Screening For Genetic Disorders In North Indian Population Reveals Unexpected Results – A Pilot Study

Journal: BMC Medical Genetics | November 2021

Author: Kanika Singh, Sunita Bijarnia-Mahay, V. L. Ramprasad, Ratna Dua Puri, Sandhya Nair, Sheetal Sharda, Renu Saxena, Sudha Kohli, Samarth Kulshreshtha, Indrani Ganguli, Kanwal Gujral And Ishwar C. Verma

Abstract:

To determine the carrier frequency and pathogenic variants of common genetic disorders in the north Indian population by using next generation sequencing (NGS). Methods After pre-test counselling, 200 unrelated individuals (including 88 couples) were screened for pathogenic variants in 88 genes by NGS technology.

Profile of Pathogenic Mutations and Evaluation of Germline Genetic Testing Criteria in Consecutive Breast Cancer Patients Treated at a North Indian Tertiary Care Center

Journal: Annals of Surgical Oncology | October 2021

Author: Abhenil Mittal, MD, DM1 , S. V. S. Deo, MS, MCh2 , Ajay Gogia, MD, DM1 , Atul Batra, MD, DM1 , Akash Kumar, MD, DM1 , Sandeep Bhoriwal, MS, MCh2 , Koushik Sinha Deb, MD3 , Ekta Dhamija, MD4 , Sanjay Thulkar, MD4 , V. L. Ramprasad, PhD5 , Olufunmilayo Olopade, MD, FACP6 , and Raja Pramanik, MD, DM1

Abstract:

The burden of hereditary breast cancer in India is not well defined. Moreover, genetic testing criteria (National Comprehensive Cancer Network [NCCN] and Mainstreaming Cancer Genetics [MCG] Plus) have never been validated in the Indian population.

Myoneuropathic presentation of limb girdle muscular dystrophy R8 with a novel TRIM32 mutation

Journal: Neuromuscular disorders | September 2021

Author: Soumya V Chandrasekharan 1, Soumya Sundaram 1, Sivasankar Malaichamy 2, Rajalakshmy Poyuran 3, Sruthi S Nair 4

Abstract:

orted in fewer than 100 patients worldwide. Here, we report a male patient with progressive proximo-distal lower limb weakness with onset in the third decade who had mixed myopathic and neurogenic pattern in

HopA1 Effector from Pseudomonas syringae pv syringae Strain 61 Affects NMD Processes and Elicits Effector-Triggered Immunity

Journal: International Journal of Molecular sciences | July 2021

Author: Shraddha K. Dahale ,Daipayan Ghosh ,Kishor D. Ingole ,Anup Chugani , Sang Hee Kim and Saikat Bhattacharjee

Abstract:

Pseudomonas syringae-secreted HopA1 effectors are important determinants in host range expansion and increased pathogenicity. Their recent acquisitions via horizontal gene transfer in several non-pathogenic Pseudomonas strains worldwide have caused alarming increase in their virulence

Phenotypic expression and clinical outcomes in a South Asian PRKAG2 cardiomyopathy cohort

Journal: Scientific reports | November 2020

Author: Hisham Ahamed , Aniketh Vijay Balegadde , Shilpa Menon , Ramesh Menon , Aishwarya Ramachandran , Navin Mathew , K U Natarajan , Indu Ramachandran Nair , Rajesh Kannan , Meghna Shankar , Oommen K Mathew , Thong T Nguyen , Ravi Gupta , Eric W Stawiski , V L Ramprasad , Somasekar Seshagiri , Sameer Phalke

Abstract:

The PRKAG2 syndrome is a rare autosomal dominant phenocopy of sarcomeric hypertrophic cardiomyopathy (HCM), characterized by ventricular pre-excitation, progressive conduction system disease and left ventricular hypertrophy. This study describes the phenotype

Ophthatome™: an integrated knowledgebase of ophthalmic diseases for translating vision research into the clinic

Journal: BMC Ophthalmology | November 2020

Author: Praveen Raj, Sushma Tejwani, Dandayudhapani Sudha, B. Muthu Narayanan, Chandrasekar Thangapandi, Sankar Das, J. Somasekar, Susmithasane Mangalapudi, Durgesh Kumar, Narendra Pindipappanahalli, Rohit Shetty, Arkasubhra Ghosh, Govindasamy Kumaramanickavel, Amitabha Chaudhuri & Nagasamy Soumittra

Abstract:

Medical big data analytics has revolutionized the human healthcare system by introducing processes that facilitate rationale clinical decision making, predictive or prognostic modelling of the disease progression and management, disease surveillance, overall impact on public health and research. Although, the electronic medical records (EMR) system is the digital

Infantile spasms: Etiology, lead time and treatment response in a resource limited setting.

Journal: Epilepsy Behav Rep. | October 2020

Author: Surana P, Symonds JD, Srivastava P, Geetha TS, Jain R, Vedant R, Murugan S, Mahalingam S, Bhargava V, Goyal P, Zuberi SM, Jain V.

Abstract:

This study explores the etiology and lead time to treatment for infantile spasm (IS) patients and their effect on treatment responsiveness, in a limited resource setting. Patients with IS onset age ≤12 months', seen over 3 years were recruited retrospectively. Clinical information, neuroimaging and genetic results retrieved.

Seven novel genetic variants in a North Indian cohort with classical homocystinuria

Journal: Nature Scientific reports | October 2020

Author: Rajdeep Kaur 1, Savita V Attri 2, Arushi G Saini 1, Naveen Sankhyan 1, Satwinder Singh 1, Mohammed Faruq 3, V L Ramprasad 4, Sheetal Sharda 4, Sakthivel Murugan 4

Abstract:

Classical homocystinuria is the most common cause of isolated homocystinuria. The variants of the CBS gene remain unidentified in Indian children with this disorder. Based on the hallmark clinical features, family history, and/or biochemical clues for classical homocystinuria

Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate

Journal: Movement disorders clinical practice | August 2020

Author: Akhilesh Pandey # 1 2 3, Eric W Stawiski # 4 5 6, Steffen Durinck # 7 8, Harsha Gowda # 9 10, Leonard D Goldstein 7 8, Mustafa A Barbhuiya 9 11, Markus S Schröder 8 12, Sreelakshmi K Sreenivasamurthy 9, Sun-Whe Kim 13, Sameer Phalke 14, Kushal Suryamohan 15, Kayla Lee 15, Papia Chakraborty 15, Vasumathi Kode 15, Xiaoshan Shi 15, Aditi Chatterjee 9, Keshava Datta 9, Aafaque A Khan 9, Tejaswini Subbannayya 9, Jing Wang 15, Subhra Chaudhuri 8, Sanjiv Gupta 16, Braj Raj Shrivastav 17, Bijay S Jaiswal 8, Satish S Poojary 18, Shushruta Bhunia 18, Patricia Garcia 19, Carolina Bizama 19, Lorena Rosa 20, Wooil Kwon 13, Hongbeom Kim 13, Youngmin Han 13, Thakur Deen Yadav 21, Vedam L Ramprasad 14, Amitabha Chaudhuri 15, Zora Modrusan 8, Juan Carlos Roa 19, Pramod Kumar Tiwari 18, Jin-Young Jang 22, Somasekar Seshagiri 23 24

Abstract:

Gallbladder cancer (GBC) is an aggressive gastrointestinal malignancy with no approved targeted therapy. Here, we analyze exomes (n = 160), transcriptomes (n = 115), and low pass whole genomes (n = 146) from 167 gallbladder cancers (GBCs) from patients in Korea, India and Chile.

A Case of Autosomal Dominant Ataxia with Vocal Cord Palsy Attributed to a Mutation in the PRNP Gene.

Journal: Mov Disord Clin Pract. | July 2020

Author: Kukkle PL, Geetha TS, Mahadevan A, Ramprasad VL.

Abstract:

Keywords: ataxia, CJD, familial, vocal cord palsy, autosomal dominant.

Validation of a Genome-Wide Polygenic Score for Coronary Artery Disease in South Asians

Journal: JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY | June 2020

Author: Minxian Wang, PHD,Ramesh Menon, PHD, Sanghamitra Mishra, PHD, Aniruddh P. Patel, MD, Mark Chaffin, MSC, Deepak Tanneeru, MTECH, Manjari Deshmukh, MSC, Oshin Mathew, MSC, Sanika Apte, MSC, Christina S. Devanboo, MSC, Sumathi Sundaram, BSC, Praveena Lakshmipathy, MSC, Sakthivel Murugan, PHD, Krishna Kumar Sharma, PHD,Karthikeyan Rajendran, BPT, Sam Santhosh, BTECH, MBA, Rajesh Thachathodiyl, MBBS, MD, Hisham Ahamed, MD, Aniketh Vijay Balegadde, MBBS, MD, Thomas Alexander, MD, Krishnan Swaminathan, MD, Rajeev Gupta, MD, PHD, Ajit S. Mullasari, MBBS, MD, Alben Sigamani, MBBS, MD, Muralidhar Kanchi, MBBS, MD, MBA, Andrew S. Peterson, PHD, Adam S. Butterworth, PHD, John Danesh, DPHIL, Emanuele Di Angelantonio, MD, PHD, Aliya Naheed, MBBS, MPH, PHD, Michael Inouye, PHD, Rajiv Chowdhury, MPH, PHD, Ramprasad L. Vedam, PHD, Sekar Kathiresan, MD, Ravi Gupta, PHD, Amit V. Khera, MD, MSC.

Abstract:

Genome-wide polygenic scores (GPS) integrate information from many common DNA variants into a single number. Because rates of coronary artery disease (CAD) are substantially higher among South Asians, a GPS to identify high-risk individuals may be particularly useful in this population.

A Rare Neurological Presentation of Familial Hemophagocytic Lymphohistiocytosis.

Journal: Journal of Pediatric Neurology | May 2020

Author: Vishal Patel, Anaita Udwadia-Hegde, Omkar Hajirnis, Tarishi Nemani, Ambreen Pandrowala

Abstract:

In this case report, we described a 15-year-old boy who presented with intermittent episodes of ataxia and diplopia since 6.5 years of age. Extensive workup done over several years was negative. Brain biopsy showed a neuroinflammatory disorder, and hence, differential diagnosis of chronic lymphocytic inflammation with pontine perivascular

Genetic analysis of familial hypercholesterolemia in Asian Indians: a single center study

Journal: Journal of Clinical Lipidology | December 2019

Author: Nitika Setia, PhD*`, Sireesha Movva, PhD, ,2, Prahlad Balakrishnan, PhD, , Ishpreet K Bij MSc, 1, JPS Sawhney, MD, DM, Raman Puri, MD, Anjali Arora, MD, Ratna D Puri, MD, DM, Renu Saxena PhD, Sanghamitra Mishra PhD, Sanika Apte MSc Samarth Kulshrestha MSc, VL Ramprasad, PhD, & Ishwar C Verma MRCP*

Abstract:

Familial Hypercholesterolemia (FH), an autosomal co-dominant disorder characterized by very high LDL cholesterol, is strongly associated with premature coronary artery disease. Molecular landscape of FH in Asian Indians is not well studied, although this ethnic group comprises a large proportion of the world population. Knowledge of mutations in these groups is useful for identifying persons affected with FH, saving their…

S100a4 upregulation in Pik3caH1047R;Trp53R270H;MMTV-Cre-driven mammary tumors promotes metastasis.

Journal: Breast Cancer Research | December 2019

Author: Yuan W1, Goldstein LD1,2, Durinck S1,2, Chen YJ1, Nguyen TT1, Kljavin NM3, Sokol ES4, Stawiski EW5, Haley B1, Ziai J6, Modrusan Z1, Seshagiri S7,8.

Abstract:

PIK3CA mutations are frequent in human breast cancer. Pik3caH1047R mutant expression in mouse mammary gland promotes tumorigenesis. TP53 mutations co-occur with PIK3CA mutations in human breast cancers. We previously generated a conditionally activatable Pik3caH1047R;MMTV-Cre mouse model and found a few malignant sarcomatoid (spindle cell) carcinomas that had acquired spontaneous dominant-negative Trp53 mutations.

MAP2K1 is a potential therapeutic target in erlotinib resistant head and neck squamous cell carcinoma

Journal: Scientific Reports volume | December 2019

Author: Ankit P. Jain, Krishna Patel, Sneha Pinto, Aneesha Radhakrishnan, Vishalakshi Nanjappa, Manish Kumar, Remya Raja, Arun H. Patil, Anjali Kumari, Malini Manoharan, Coral Karunakaran, Saktivel Murugan, T. S. Keshava Prasad, Xiaofei Chang, Premendu Prakash Mathur, Prashant Kumar, Ravi Gupta, Rohit Gupta, Arati Khanna-Gupta, David Sidransky, Aditi Chatterjee & Harsha Gowda

Abstract:

Epidermal growth factor receptor (EGFR) targeted therapies have shown limited efficacy in head and neck squamous cell carcinoma (HNSCC) patients despite its overexpression. Identifying molecular mechanisms associated with acquired resistance to EGFR-TKIs such as erlotinib remains an unmet need and a therapeutic challenge.

Association of HLA-A, -B, DRB, and DQB Alleles with Persistent HPV-16 Infection in Women from Tamil Nadu, India

Journal: Viral Immunology | December 2019

Author: Muthumeenakshi Bhaskaran, Sree Varshini Murali, Barathi Rajaram, Sundar Krishnasamy, C.S. Devasena, Atima Pathak, Vidhya Ravi, Krishnan Swaminathan, Ashok Ayyappa, Srinivasan Vedhantham, Arun Seshachalam, and GaneshPrasad ArunKumar

Abstract:

Women with persistent human papillomavirus (HPV) infections have a high risk of developing cervical cancer (CaCx). HPV-16 alone accounts for more than 60% of CaCx worldwide. Most of the HPV infections are transient and only a subset of women develop persistent HPV-16 infection.

Prevalence of mutations in inherited retinal diseases: A comparison between the United States and India

Journal: Molecular Genetics and Genomic Medicine | December 2019

Author: Sophia Yohe Malaichamy Sivasankar Anuprita Ghosh Arkasubhra Ghosh Jennifer Holle Sakthivel Murugan Ravi Gupta Lisa A. Schimmenti Ramprasad Vedam Bharat Thyagarajan

Abstract:

Studies evaluating next‐generation sequencing (NGS) for retinal disorders may not reflect clinical practice. We report results of retrospective analysis of patients referred for clinical testing at two institutions (US and India). Methods This retrospective study of 131 patients who underwent clinically

Prevalence of mutations in inherited retinal diseases: A comparison between the United States and India

Journal: Molecular Genetics and Genomic Medicine | December 2019

Author: Sophia Yohe Malaichamy Sivasankar Anuprita Ghosh Arkasubhra Ghosh Jennifer Holle Sakthivel Murugan Ravi Gupta Lisa A. Schimmenti Ramprasad Vedam Bharat Thyagarajan

Abstract:

Studies evaluating next‐generation sequencing (NGS) for retinal disorders may not reflect clinical practice. We report results of retrospective analysis of patients referred for clinical testing at two institutions (US and India). Methods This retrospective study of 131 patients who underwent clinically validated targeted NGS or exome sequencing for a wide variety of clinical

Identification of African-Specific Admixture between Modern and Archaic Humans

Journal: The American Journal of Human Genetics | December 2019

Author: Jeffrey D. Wall Aakrosh Ratan Eric Stawiski the GenomeAsia 100K Consortium

Abstract:

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require…

The GenomeAsia 100K Project enables genetic discoveries across Asia

Journal: Nature | December 2019

Author: Jeffrey D. Wall, Eric W. Stawiski, Aakrosh Ratan, Hie Lim Kim, Changhoon Kim, Ravi Gupta, Kushal Suryamohan, Elena S. Gusareva, Rikky Wenang Purbojati, Tushar Bhangale, Vadim Stepanov, Vladimir Kharkov, Markus S. Schröder, Vedam Ramprasad, Jennifer Tom, Steffen Durinck, Qixin Bei, Jiani Li, Joseph Guillory, Sameer Phalke, Analabha Basu, Jeremy Stinson, Sandhya Nair, Sivasankar Malaichamy, Nidhan K. Biswas, John C. Chambers, Keith C. Cheng, Joyner T. George, Seik Soon Khor, Jong-Il Kim, Belong Cho, Ramesh Menon, Thiramsetti Sattibabu, Akshi Bassi, Manjari Deshmukh, Anjali Verma, Vivek Gopalan, Jong-Yeon Shin, Mahesh Pratapneni, Sam Santhosh, Katsushi Tokunaga, Badrul M. Md-Zain, Kok Gan Chan, Madasamy Parani, Purushothaman Natarajan, Michael Hauser, R. Rand Allingham, Cecilia Santiago-Turla, Arkasubhra Ghosh, Santosh Gopi Krishna Gadde, Christian Fuchsberger, Lukas Forer, Sebastian Schoenherr, Herawati Sudoyo, J. Stephen Lansing, Jonathan Friedlaender, George Koki, Murray P. Cox, Michael Hammer, Tatiana Karafet, Khai C. Ang, Syed Q. Mehdi, Venkatesan Radha, Viswanathan Mohan, Partha P. Majumder, Somasekar Seshagiri, Jeong-Sun Seo, Stephan C. Schuster & Andrew S. Peterson - Nature volume 576, pages106 – 111(2019)

Abstract:

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue.

A Computational Approach Identifies Immunogenic Features of Prognosis in Human Cancers.

Journal: Frontiers of Immunology | December 2018

Author: Malini Manoharan, Nitin Mandloi, Sushri Priyadarshini, Ashwini Patil, Rohit Gupta, Laxman Iyer, Ravi Gupta and Amitabha Chaudhuri

Abstract:

A large number of tumor intrinsic and extrinsic factors determine long-term survival in human cancers. In this study, we stratified 9120 tumors from 33 cancers with respect to their immune cell content and identified immunogenomic features associated with long-term survival.

Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma.

Journal: Febs Letters | November 2018

Author: Swagatika Sahoo Ranjith Kumar Ravi Kumar Brandon Nicolay Omkar Mohite Karthikeyan Sivaraman Vikas Khetan Pukhraj Rishi Suganeswari Ganesan Krishnakumar Subramanyan Karthik Raman Wayne Miles Sailaja V. Elchuri

Abstract:

Retinoblastoma (RB) is a childhood eye cancer. Currently, chemotherapy, local therapy, and enucleation are the main ways in which these tumors are managed. The present work is the first study that uses constraint‐based reconstruction and analysis approaches to identify and explain RB‐specific survival strategies, which are RB tumor

Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations

Journal: Cancer cells | October 2018

Author: Kanika Bajaj Pahuja,Thong T. Nguyen ,Bijay S. Jaiswal ,Kumar Prabhash ,Tarjani M. Thaker ,Kate Senger,Subhra Chaudhuri,Noelyn M. Kljavin,Aju Antony,Sameer Phalke,Prasanna Kumar, Marco Mravic,Eric W. Stawiski,Derek Vargas,Steffen Durinck,Ravi Gupta,Arati Khanna-Gupta,Sally E. Trabucco,Ethan S. Sokol,Ryan J. Hartmaier, Ashish Singh, Anuradha Chougule, Vaishakhi Trivedi, Amit Dutt, Vijay Patil, Amit Joshi, Vanita Noronha, James Ziai, Sripad D. Banavali, Vedam Ramprasad William F. DeGrado, Raphael Bueno, Natalia Jura, Somasekar Seshagiri

Abstract:

Deregulated HER2 is a target of many approved cancer drugs. We analyzed 111,176 patient tumors and identified recurrent mutations in HER2 transmembrane domain (TMD) and juxtamembrane domain (JMD) that include G660D, R678Q, E693K, and Q709L. Using a saturation mutagenesis screen and testing of patient-derived mutations we found several activating TMD and JMD mutations.

Is there a Chance to Promote Arteriogenesis by DPP4 Inhibitors Even in Type 2 Diabetes? A Critical Review.

Journal: Cells | October 2018

Author: Srinivasan Vedantham, Anna-Kristina Kluever and Elisabeth Deindl

Abstract:

Cardiovascular diseases (CVD) are still the prevailing cause of death not only in industrialized countries, but even worldwide. Type 2 diabetes mellitus (type 2 DM) and hyperlipidemia, a metabolic disorder that is often associated with diabetes, are major risk factors for developing CVD. Recently, clinical trials proved the safety of gliptins in treating patients with type 2 DM.

A neoepitope derived from a novel human germline APC gene mutation in familial adenomatous polyposis shows selective immunogenicity

Journal: Plos One | September 2018

Author: Snigdha Majumder ,Rakshit Shah ,Jisha Elias,Yogesh Mistry,Karunakaran Coral,Priyanka Shah,Anand Kumar Maurya,Bharti Mittal,Jason K. D’Silva,Sakthivel Murugan,Lakshmi Mahadevan,Rekha Sathian,V. L. Ramprasad, [ ... ],Arati Khanna-Gupta

Abstract:

Familial adenomatous polyposis (FAP) is an inherited condition arising from genetic defects in the Adenomatous polyposis coli (APC) gene. Carriers with mutations in the APC gene develop polyps in the colon and rectum which if not managed, transition into colon cancer. In this study, we identified a novel germline mutation in the APC gene in members of an FAP-affected (Familial…

Progressive nonparoxysmal chorea and dystonia due to myofibrillogenesis regulator-1 gene mutation

Journal: Parkinsonism & Related Disorders | August 2018

Author: Sanjay Pandey Laxmikant Ramkumarsingh Tomar Lakshmi Mahadevan

Abstract:

Mutations in the myofibrillogenesis regulator gene (MR-1) causes paroxysmal non -kinesigenic dyskinesia (PNKD) characterized by episodic (paroxysmal) attacks of any combination of chorea, dystonia and athetosis ( MR-1/PNKD) [ 1 ]. This gene is transcribed into three alternatively spliced isoforms: long (MR-1L), medium (MR-1M) and small (MR-1S) [ 2 , 3 ].

A cancer vaccine approach for personalized treatment of Lynch Syndrome

Journal: Nature | August 2018

Author: Snigdha Majumder, Rakshit Shah, Jisha Elias, Malini Manoharan, Priyanka Shah, Anjali Kumari, Papia Chakraborty, Vasumathi Kode, Yogesh Mistry, Karunakaran Coral, Bharti Mittal, Sakthivel Murugan SM, Lakshmi Mahadevan, Ravi Gupta, Amitabha Chaudhuri & Arati Khanna-Gupta

Abstract:

Snigdha Majumder, Rakshit Shah, Jisha Elias, Malini Manoharan, Priyanka Shah, Anjali Kumari, Papia Chakraborty, Vasumathi Kode, Yogesh Mistry, Karunakaran Coral, Bharti Mittal, Sakthivel Murugan SM, Lakshmi Mahadevan, Ravi Gupta, Amitabha Chaudhuri & Arati Khanna-Gupta. Lynch Syndrome (LS) is an inherited heterozygous

Identification of deletion-duplication in HEXA gene in five children with Tay-Sachs disease from India

Journal: BMC Medical Genetics | July 2018

Author: Jayesh Sheth, Mehul Mistri, Lakshmi Mahadevan, Sanjeev Mehta, Dhaval Solanki, Mahesh Kamate & Frenny Sheth

Abstract:

Background Tay-Sachs disease (TSD) is a sphingolipid storage disorder caused by mutations in the HEXA gene. To date, nearly 170 mutations of HEXA have been described, including only one 7.6 kb large deletion. Methods Multiplex Ligation-dependent Probe Amplification (MLPA) study was carried out in 5 unrelated patients for copy number

A novel splice variant in EMC1 is associated with cerebellar atrophy, visual impairment, psychomotor retardation with epilepsy

Journal: Molecular Genetics and Genomic Medicine | December 2017

Author: Thenral S. Geetha Lokesh Lingappa Abhishek Ravindra Jain Hridya Govindan Nitin Mandloi Sakthivel Murugan Ravi Gupta and Ramprasad Vedam

Abstract:

Background Several genes have been implicated in a highly variable presentation of developmental delay with psychomotor retardation. Mutations in EMC1 gene have recently been reported. Herein, we describe a proband born of a consanguineous marriage, who presented with early infantile onset epilepsy, scaphocephaly, developmental delay, central hypotonia, muscle wasting, and severe cerebellar and brainstem atrophy.

Serum starvation of ARPE-19 changes the cellular distribution of cholesterol and Fibulin3 in patterns reminiscent of age-related macular degeneration

Journal: Experimental cell research | December 2017

Author: Dinusha Rajapakse 1, Katherine Peterson 2, Sanghamitra Mishra 3, Graeme Wistow 4

Abstract:

Retinal pigment epithelium (RPE) has been implicated as key source of cholesterol-rich deposits at Bruch's membrane (BrM) and in drusen in aging human eye. We have shown that serum-deprivation of confluent RPE cells is associated with upregulation of cholesterol synthesis and accumulation of unesterified cholesterol (UC).

Asparagine Synthetase deficiency-report of a novel mutation and review of literature

Journal: Metabolic Brain Disease | August 2017

Author: Neerja Gupta, Vishal Vishnu Tewari, Manoj Kumar, Nitika Langeh, Aditi Gupta, Pallavi Mishra, Punit Kaur, Vedam Ramprasad, Sakthivel Murugan, Reema Kumar, Manisha Jana & Madhulika Kabra

Abstract:

Asparagine synthetase deficiency is a rare inborn error of metabolism caused by a defect in ASNS, a gene encoding asparagine synthetase. It manifests with a severe neurological phenotype manifesting as severe developmental delay, congenital microcephaly, spasticity and refractory seizures. To date, nineteen patients from twelve unrelated families have been identified. Majority of the

Autosomal Recessive Spastic Ataxia of Charlevoix‐Saguenay (ARSACS)–First Report of Clinical and Imaging Features from India, and a Novel SACS Gene Duplication

Journal: Movement disorders- Clinical Practice | July 2017

Author: Pankaj A. Agarwal MD, DNB, DM, Priti Ate‐Upasani MD, DNB, DMRE and Vedam L. Ramprasad PhD

Abstract:

Autosomal recessive spastic ataxia of Charlevoix‐Saguenay (ARSACS) was described by Bouchard and colleagues in 1978 from Quebec, Canada, as a rare cause of autosomal recessive cerebellar ataxia. 1.2 Subsequent reports confirmed the presence of this condition in other parts of the world, including Europe and, in Asia, Japan.

Next-Generation Sequencing Reveals Novel Mutations in X-linked Intellectual Disability

Journal: Journal of Integrative Biology | May 2017

Author: Babylakshmi Muthusamy, Lakshmi Dhevi N. Selvan, Thong T. Nguyen, Jesna Manoj, Eric W. Stawiski, Bijay S. Jaiswal, Weiru Wang, Remya Raja, Vedam Laxmi Ramprasad, Ravi Gupta, Sakthivel Murugan, Jayarama S. Kadandale, T.S. Keshava Prasad, Kavita Reddy, Andrew Peterson, Akhilesh Pandey, Somasekar Seshagiri, Satish Chandra Girimaji, and Harsha Gowda

Abstract:

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

Mycobacterium tuberculosis in Wild Asian Elephants, Southern India

Journal: Emerging Infectious Diseases | March 2017

Author: Arun Zachariah, Jeganathan Pandiyan, G.K. Madhavilatha, Sathish Mundayoor, Bathrachalam Chandramohan, P.K. Sajesh, Sam Santhosh, and Susan K. Mikota

Abstract:

We tested 3 ild Asian elephants (Elephas maximus) in southern India and confirmed infection in 3 animals with Mycobacterium tuberculosis, an obligate human pathogen, by PCR and genetic sequencing. Our results indicate that tuberculosis may be spilling over from humans (reverse zoonosis) and emerging in wild elephants.

The utility and futility of targeted Next-generation sequencing for carrier detection in ‘At Risk’ couples

Journal: The Indian Academy of Medical Genetics (IAMG) | January 2017

Author: Sunita Bijarnia-Mahay 1*, Deepti Gupta 1, V L Ramprasad 2, Sakthivel Murugan 2 , Renu Saxena 1, Sudha Kohli 1, Seiji Yamaguchi 3, Yosuke Shigematsu 4 and I C Verma 1

Abstract:

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…

Predicting Response to Immunosuppressive Therapy in Patients with Acquired Aplastic Anemia using EGFR and TWIST1 Expression Levels

Journal: Blood | December 2016

Author: Sharat Damodar, Varun Bafna, Arati Khanna-Gupta,Shilpa Prabhu, Nataraj KS, Durga Sarvepalli, PhD, Snigdha Majumder, Coral Karunakaran, Malini Manoharan, Sakthivel Murugan, Chirantan Bose, Ravi Gupta, Arkasubhra Ghosh

Abstract:

EGFR (epidermal growth factor receptor) is important for the proliferation of stem cells across the body including the hematopoietic niche. However, the role of EGFR in aplastic anemia and subsequent responses to standard-of-care therapy is unknown.TWIST is a basic helix-loop-helix transcription factor recently found to regulate the hematopoietic stem cell (HSC) niche.

Manitoba Oculotrichoanal Syndrome: First case report from India

Journal: Delhi Journal of Ophthalmology | September 2016

Author: Sai Rani Karanam, Vinay Kumar Konana, Shruthi Sreenivasaiah, Sudhakar Potti

Abstract:

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.

A splice site mutation in HERC1 leads to Syndromic Intellectual Disability with macrocephaly and facial dysmorphism: Further delineation of the phenotypic spectrum

Journal: NCBI | April 2016

Author: Aggarwal S, Bhowmik AD, Ramprasad VL, Murugan S, Dalal A

Abstract:

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

The expression dynamics of mechanosensitive genes in extra-embryonic vasculature after heart starts to beat in chick embryo

Journal: Biorheology | April 2016

Author: Rajendran Saranyaa, Sundaresan Lakshmikirupaa, Rajendran Krithikaa, Selvaraj Monica, Gupta Ravi Chatterjee, Suvro.

Abstract:

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…

Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations

Journal: Nature Genetics | February 2016

Author: Raphael Bueno, Eric W Stawiski, Leonard D Goldstein, Steffen Durinck, Assunta De Rienzo, Zora Modrusan, Florian Gnad, Thong T Nguyen, Bijay S Jaiswal, Lucian R Chirieac, Daniele Sciaranghella, Nhien Dao, Corinne E Gustafson, Kiara J Munir, Jason A Hackney, Amitabha Chaudhuri, Ravi Gupta, Joseph Guillory, Karen Toy, Connie Ha, Ying-Jiun Chen, Jeremy Stinson, Subhra Chaudhuri, Na Zhang, Thomas D Wu, David J Sugarbaker, Frederic J de Sauvage, William G Richards & Somasekar Seshagiri

Abstract:

We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated…

A novel H395R mutation in MKKS/BBS6 causes retinitis pigmentosa and polydactyly without other findings of Bardet-Biedl or McKusick-Kaufman syndrome

Journal: Molecular Vision | January 2016

Author: John D. Hulleman, Annie Nguyen, V.L. Ramprasad, Sakthivel Murugan, Ravi Gupta, Avinash Mahindrakar, Ravi Angara, Chandrasekhar Sankurathri, and V. Vinod Mootha

Abstract:

To identify the causative mutation in two siblings from a consanguineous family in India with retinitis pigmentosa (RP) and polydactyly without other findings of Bardet-Biedl syndrome (BBS). We also performed functional characterization of the mutant protein to explore its role in this limited form of BBS. Methods The siblings underwent a thorough ophthalmological examination, including retinal optical coherence tomography (OCT)…

First Report of Kufor‐Rakeb Syndrome (PARK 9) from India, and a Novel Nonsense Mutation in ATP13A2 Gene

Journal: Movement disorders- Clinical Practice | May 2015

Author: L.K. Prashanth DM, Sakthivel Murugan PhD, Vikram Kamath DM, Ravi Gupta PhD, Rakesh Jadav MD, DM, S. Sreekantaswamy MD, DM and Vedam L. Ramprasad PhD

Abstract:

Kufor‐Rakeb syndrome (KRS; PARK 9) is a rare autosomal‐recessive form of juvenile‐onset Parkinson's disease (PD) caused by ATP13A2 gene mutations. The classical description of KRS is that of rapidly progressive symptoms in the form of parkinsonism, spasticity, supranuclear upgaze paresis, facial‐faucial‐finger minimyoclonus, visual hallucinations, oculogyric dystonic spasms, and

Identification of Novel Mutations in ABCA4 Gene: Clinical and Genetic Analysis of Indian Patients with Stargardt Disease.

Journal: BioMed Research International | April 2015

Author: Rajani Battu, Anshuman Verma, Ramesh Hariharan, Shuba Krishna, Ravi Kiran, Jemima Jacob, Aparna Ganapathy, Vedam L. Ramprasad, Govindasamy Kumaramanickavel, Nallathambi Jeyabalan , and Arkasubhra Ghosh

Abstract:

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.

Evolution of targeted therapies in cancer: opportunities and challenges in the clinic

Journal: Future Oncology | January 2015

Author: Sam Santhosh, Prasanna Kumar, Vedam Ramprasad & Amitabha Chaudhuri

Abstract:

Targeted therapies have changed the course of cancer treatment in recent years. By reducing toxicity and improving outcome, these new generations of precision medicines have extended patient lives beyond what could be achieved by the use of nontargeted therapies. In the last 2 years, several new molecular entities targeting signaling proteins and immune pathways have gone through successful clinical development…

Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries

Journal: Journal of Antimicrobial Chemotherapy | December 2014

Author: Halime Ekici 1, Shwetha D Rao 2, Anders Sönnerborg 3, Vedam L Ramprasad 4, Ravi Gupta 4, Ujjwal Neogi 5

Abstract:

Increased trends of primary drug resistance mutations (DRMs) among treatment-naive HIV-1-infected patients in low- and middle-income countries (LMICs) and the non-availability of pre-antiretroviral therapy (ART) genotypic resistance testing (GRT) may severely affect future therapeutic outcomes. The main objective of this study was therefore to develop a simplified, cost- and labour-efficient but high-throughput GRT protocol to

Regulation of Macrophage Polarization by RON Receptor Tyrosine Kinase Signaling.

Journal: Frontiers in Immunology | October 2014

Author: Chaudhuri A1

Abstract:

The M1 and M2 states of macrophage polarization are the two extremes of a physiologic/phenotypic continuum that is dynamically influenced by environmental signals. The M1/M2 paradigm is an excellent framework to understand and appreciate some of the diverse functions that macrophages perform. Molecular analysis of mouse and human macrophages indicated that they gain M1 and M2-related functions after encountering specific…

Prevalence of genetic variants associated with cardiovascular disease risk and drug response in the Southern Indian population of Kerala

Journal: Indian Journal of Human Genetics | June 2014

Author: Lakshmi Mahadevan, Ancy Yesudas, P. K. Sajesh, S. Revu, Prasanna Kumar, Devi Santhosh, Sam Santhosh, J. M. Sashikumar, V. K. Gopalakrishnan, Joji Boben, and Changanamkandath Rajesh

Abstract:

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.

Recessive mutations in SLC38A8 cause Foveal Hypoplasia and Optic Nerve Misrouting without Albinism

Journal: The American Journal Of Human Genetics | November 2013

Author: James A. Poulter, Musallam Al-Araimi, Ivan Conte, Maria M. van Genderen, Eamonn Sheridan, Ian M. Carr, David A. Parry, Mike Shires, Sabrina Carrella, John Bradbury, Kamron Khan, Phillis Lakeman, Panagiotis I. Sergouniotis, Andrew R. Webster, Anthony T. Moore, Bishwanath Pal, Moin D. Mohamed, Anandula Venkataramana, Vedam Ramprasad, Rohit Shetty, Murugan Saktivel, Govindasamy Kumaramanickavel, Alex Tan, David A. Mackey, Alex W. Hewitt, Sandro Banfi, Manir Ali, Chris F. Inglehearn, and Carmel Toomes (2013). The American Journal of Human Genetics, 93, 1143–1150.

Abstract:

Foveal hypoplasia and optic nerve misrouting are developmental defects of the visual pathway and only co-occur in connection with albinism; to date, they have only been associated with defects in the melanin-biosynthesis pathway. Here, we report that these defects can occur independently of albinism in people with recessive mutations in the putative glutamine transporter gene SLC38A8.

Sequencing and analysis of a South Asian-Indian personal genome

Journal: BMC Genomics | August 2012

Author: Ravi Gupta, Aakrosh Ratan, Changanamkandath Rajesh, Rong Chen, Hie Lim Kim, Richard Burhans, Webb Miller, Sam Santhosh, Ramana V Davuluri, Atul J Butte, Stephan C Schuster, Somasekar Seshagiri and George Thomas (2012). BMC Genomics, 13, 440.

Abstract:

With over 1.3 billion people, India is estimated to contain three times more genetic diversity than Europe. Next-generation sequencing technologies have facilitated the understanding of diversity by enabling whole genome sequencing at greater speed and lower cost. While genomes from people of European and Asian descent have been sequenced, only recently has a single male genome from the

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