Siddharth Banka, MBBS MRCPCH PhD

Prof, MBBS, MRCPCH, CCT (Clinical Genetics), PhD

Personal profile

Qualifications

  • PhD (University of Manchester)
  • CCST in Clinical Genetics (UK)
  • MRCPCH (UK)
  • MBBS (University of Mumbai)

Overview

Rare diseases pose a significant medical and societal challenge because they affect ~5% of the population. A vast majority of rare diseases are genetic in origin. Rare Diseases are often difficult to define, diagnose, manage and treat.

I am a Clinician Scientist who combines genomics with functional and clinical studies in rare human genetic disorders.  My current research programs have following themes - (1) performing systematic analysis of whole genome data to discover novel diseases; (2) understanding the mechanisms of paediatric disorders of chromatin remodelling and inborn errors of metabolism to develop new treatments; (3) understanding the contribution of copy number and non-coding variants in Mendelian disorders; and (4) establishing cohorts of paitents with rare disorders for natural history studies and clinical trials.

I hold a joint position at the Manchester Centre for Genomic Medicine (Manchester University NHS Trust) as a Consultant Clinical Geneticist. In my clinical prcatice I see children and adults with a range of genetic disorders.

I am the Founding Clinical Director of the Manchester Rare Conditions Centre.

Overall, the aim of my work is to improve diagnosis, management and treatment of rare diseases. 

Biography

I graduated in Medicine (MBBS) from Lokmanya Tilak Medical College (University of Mumbai) in 2002, obtained Membership of Royal College of Paediatrics and Child Health (MRCPCH) in 2006 and joined Clinical Genetics training programme in Manchester in 2007. I was awarded a Research Training Fellowship by the NIHR Manchester Biomedical Research Centre from 2008 to 2011 and was awarded PhD by the University of Manchester in 2012. I obtained my Certificate of Completion of Specialist Training (CCST) in Clinical Genetics training in 2013 and was subsequently appointed as Clinical Senior Lecturer and Consultant Clinical Geneticist in July 2013. I have been in my current position from 2021.

Research interests

Rare genetic conditions collectively affect approximately 5% of the population. More than 50% patients with suspected genetic disorders remain unsolved even after whole genome sequencing. Furthermore, for disorders with known genetic causes, the management and treatment options are usually limited.

Identification of novel diseases

We have led on, or played a major role in, the identification of several rare genetic diseases and uncovered their mechanisms –

We have also contributed to collaborative projects leading to the discoveries of following diseases -

Current work: We are performing systematic analysis of whole genome/exome data from several thousand patients with unsolved genetic disorders. This work is being done in collaboration with large national and international projects such as the 100,000 Genomes Project, Solve-RD, the Deciphering Developmental Disorders study and the Genomics of Developmental Disorders in India project. We are specially interested in disorders caused by variants in genes encoding components of the chromatin machinary and in identification of disease-causing cryptic and non-coding variants.

Uncovering rare-diseases mechanisms

In collaboration with several research groups, locally and internationally, we have used cellular and organismal models to understand mechanisms of several diseases that has provided insights into fundamental biological processes (e.g. nuclear role of beta-actin and the role of POU3F2 in the neuroendocrine pathway for appetite); showed the diversity of disease causing genetic mechanisms (e.g. extreme phenotypic variability in RAC1-associated intellectual disability) and highlighted link of rare disease genes with commoner conditions (e.g. Leri’s pleonosteosis and systemic sclerosis); and led to development of treatments for some rare disorders (e.g. folinic acid treatment for DHFR deficiency).

Current work: We are using induced pluripotent stem cells (iPSCs) to study the basis of neuroloical disease (differentiating into cortical neurons) and malformations (differentiating into neural crest cells) in diseases caused by KMT2D mutations (with Prof Sue Kimber); Drosophila models to study the mechanism of RAC-related disorder (with Dr Tom Millard); zebrafish models to study EIF5A, FKBP4 and RLF-related disorders (with Dr Paul Kasher); mice models to study ACTB-related disordes (with Prof Adrian Woolf).    

Clinical and molecular spectrum characterisation and guidelines development

Knowing phenotypic spectrum of rare conditions is crucial for their diagnosis and management. We have led on, or played a major role in, clinical characterisation of the following diseases -

  • TSPEAR-related Ectodermal dysplasia 14 (PMID 37009414)
  • KMT5B-related dominant overgrowth syndrome (PMID 36897941)
  • Diseases caused by variants in genes encoding basement membrane components (PMID - 35584218)
  • TMEM260-related Structural heart defects and renal anomalies syndrome (PMID - 34612517)
  • SETD1B-related intellectual developmental disorder with seizures and language delay (PMID - 34345025)
  • KCNT2-related Developmental and epileptic encephalopathy 57 (PMID - 34061450)
  • KDM6A-related X-linked Kabuki syndrome Type 2 (PMIDs - 33674768 and 24527667)
  • BCAT2-related Hypervalinemia or hyperleucine-isoleucinemia (PMID - 31177572)
  • Exon 30/31 CREBBP missense variants related Menke Hennekam syndrome (PMID - 30892814)
  • KMT2D and KDM6A related Kabuki syndromes (PMID - 30514738)
  • We have published the largest studies on Type 1 and Type 2 Kabuki syndromes, one of the commonest chromatin developmental disorders.
  • INPP5E-related Joubert syndrome type 1 and MORM syndrome (PMID 26748598)
  • TPK1-related episodic encephalopathy thiamine metabolism dysfunction (OMIM 614458) and Leigh syndrome. We also showed that timely treatment with thiamine supplementation improves outcome (see details).
  • We have shown that G6PC3 deficiency occurs in a phenotypic continuum and is characterized by severe congenital neutropenia with other haematological, urogenital and cardiovascular defects (see details).

We have also contributed to clinical characterisation of -

  • FZD5-related eye malformation (PMID - 36695497)
  • GBA1-related Gausher syndrome (PMID - 36537898)
  • Urorectal septum malformation syndrome (PMID - 36478354)
  • CLCN4-related Raynaud-Claes syndrome (PMID - 36385166)
  • SPTAN1-related neurogenetic disorders (PMID - 36331550)
  • Variants in BMP signalling pathway in lambdoid craniosynostosis (PMID 35997807)
  • Monogenic disorders mimicking juvenile idiopathic arthritis (PMID 35717242)
  • Exon 38/39 KMT2D misense variants related malformation disorder (PMID - 35060672)
  • Robinow syndrome (PMID 35047859)
  • HYAL2 deficiency (PMID 34906488)
  • Gaucher diseases (PMID 34649574)
  • GRIN1-related Developmental and epileptic encephalopathy (PMID 34611970)
  • Non-coding MEF2C disease-causing variants (PMID 34022131)
  • DHX30-related neurodevelopmental disorder (PMID 34020708)
  • MED12-related neurodevelopmental disorders (PMID 33244165)
  • CYFIP2-related developmental and epileptic encephalopathy 65 (PMID 33149277)
  • THOC2-related X-linked neurodevelopmental disorder (PMID 32116545)
  • CUBN-related Imerslund-Grasbeck syndrome (PMID 31497480)
  • HIST1H1E-related Rahman syndrome (PMID 31400068)
  • COL13A1-related Congenital myasthenic syndrome type 19 (PMID 31081514)
  • KMT2A-related Wiedemann-Steiner syndrome (PMID 30159147)
  • AIRE-related Autoimmune polyendocrinopathy type 1 (PMID 26084028)
  • KAT6B-related neurodevelopmental disorders (PMID 25424711)
  • TNNT3-related distal arthropgryposis type 2B2 (PMID 25337069)
  • EZH2-related Weaver syndrome (PMID 24214728)
  • PMP22-related Charcot-Marie-Tooth disease type 1A (PMID 22996176)
  • Trisomy 18 (PMID 22105572)

Current work: We are working on delineating phenotypic spectrum of several recently discovered chromatin remodelling disorders. This includes a national project on chromatin disorders as part of the NIHR BioResource for Rare Diseases. We are developing an international Expert-consensus management guidelines for Kabuki syndrome type 1. We are also a centre for a commercial clinical trial for Rett syndrome.

Functional Genomics and Advanced Diagnostics

In collaboration with EpiSigns, we have established DNA methylation arrays as a diagnotic service for rare diseases (EpiPro Project). We have also used this approach for disease identification and characterisation in research. See examples of our own and collaborative works - PMID 35904121, 35506254, 35047860, 34750377, and 31949313.

Clinical Trials

We have run clinical trials for rare diseases. See examples -

Current work - Double-blind randomised placebo-controlled dose escalation safety, tolerability and efficacy study of Blarcamesine in children with Rett syndrome

Manchester Rare Conditions Centre

The Manchester Rare Conditions Centre (MRCC) aims to improve the lives of individuals with rare diseases by providing a platform for the coordination of clinical care, research, education and engagement. See details here - MRCC website

Memberships of committees and professional bodies

  • Clinical Genetics Society (UK) - Academic Vice President
  • British Society of Genomic Medicine
  • European Society of Human Genetics
  • American Society of Human Genetics
  • British Inherited Metabolic Diseases Group
  • Skeletal Dysplasia Group
  • Royal College of Paediatrics and Child Health
  • General Medical Council

Teaching

Postgraduate University Courses

  • MRes Precision Medicine (previously Translational Medicine) project supervisor.
  • MSc Genomic Medicine project supervisor.
  • MRes Bioinformatics and Systems Biology project supervisor.
  • Faculty for PGCert Clinical Genetics and Genetic Counselling (Beijing).
  • Previous Program Director and Pathway lead for the national Genomics Scientist training program (STP) MSc.
  • Previous Clinical lead of ‘Omics Techniques and their Application to Genomic Medicine’ Module for MSc Genomic Medicine at the University of Manchester.

Undergraduate University Courses

Specialist International Courses

  • Co-organizer of the annual European Society of Human Genetics Manchester Dysmorphology course.
  • I regularly organise or teach at various international specialty training courses.

 

My collaborations

Post-doctoral Research Associates

  • Dr Sara Cuvertino (Pluripotent stem cell models of KMT2-diseases, GOSH-Sparks)
  • Dr Rebecca Yarwood (Zebrafish models of neurodegenerative disorders of Kennedy pathway, Spastic Paraplegia Foundation, USA)

 Current PhD (or equivalent) students (Primary supervisor)

  • Dr Alex Blakes (Gene termini variants in human diseases, Wellcome 4WardNorth doctoral training program)
  • Jacob Sampson (Regulatory variants in human diseases, MRC doctoral training program)
  • Shige Wang (Understanding and treating neurogenetic disorders caused by defects in the Kennedy pathway, China Scholarhip Council)
  • Evgenii Martirosian (Genomics and epigenomics of rare diseases)
  • Ankur Charasia (Genomics of Developmental Disorders in India, GCRF)
  • Emma Stevenson (Laboratory diagnosis of cobalamin deficiency, DClinSci)

Current PhD (or equivalent) students (Co-supervisor)

  • Hebah Al Thebaiti (University of Jeddah scholarship)
  • Celia Duff-Farrier (DClinSci)
  • Hilmar Orn Gunnlaugsson Nielsen (University of Iceland)
  • Rob Harkness (Wellcome DTP)
  • Carolina Stambouild (MRC DTP)

Past PhD (or equivalent) students

  • Dr Adam Jackson (Solve-RD, H2020) - Now Academic Clinical Fellow in Clinical Genetics, Manchester Centre for Genomic Medicine.
  • Ronnie Wright (Solving the unsolved via WGS, DClinSci) - Now Deputy Lead Rare Diseases Genomics, Manchester Univeristy Hospitals NHS Trust
  • Andrew Thom (Non-muscle actinopathies, Marsh studentship)
  • Dr George Burghel (Improving interpretation of CNVs, DClinSci) - Now Deputy Lead Cancer Genomics, Manchester Univeristy Hospitals NHS Trust
  • Dr Victor Faundes Gomez (Histone lysine methylases and demethylases in developmental disorders) - Now Assistant Professor at University of Santiago, Chile.
  • Dr Aimee Donald (Gaucher syndrome) - Now NIHR Academic Clinical Lecturer in Paediatric Neurology, Manchester.

 Collaborators

  • Prof Sue Kimber (iPSC models of KMT2-diseases; Manchester; Funded by GOSH-Sparks).
  • Prof Jill Clayton-Smith (Genetic basis of rare disorders; Manchester; Funded by H2020)
  • Prof Martin Lowe (Zebrafish models of Kennedy pathway disorders; Manchester; Funded by Spastic Paraplegia Foundation, USA)
  • Prof Anna Nicolaou (Lipidomics of Kennedy pathway disorders; Manchester; Funded by Spastic Paraplegia Foundation, USA)
  • Dr Tom Millard  (Drosophila models of RAC-related disorder; Manchester)
  • Dr Paul Kasher (Zebrafish models of EIF5A, FKBP4 and RLF-related disorders; Manchester; Funded by MRC DTP and H2020)
  • Prof Adrian Woolf (Mice models of ACTB-related disordes; Manchester; Funded by Marsh studentship)
  • Dr Adam Stevens (Systems biology of chromatin disorders; Manchester; Funded by GOSH-Sparks)
  • Prof Graham Pavitt (Yeast models of EIF5A; Manchester; Funded by MRC DTP)
  • Prof Colin Johnson (Ex38/39 KMT2D MV disorder; Leeds)
  • Prof Girish Katta (Genomics of Developmental Disorders in India; Manipal, India; Funded by Global Challenges Research Fund)
  • Dr Nataliya Di Donoato (ACTB-related disorders; Dresden, Germany; Funded by Marsh studentship)
  • David Gokhale (DNA methylation based diagnostics for rare diseases; Funded by GMSA)

Prizes and awards

  • Dickinson Trust Travel award in 2014 for travel to John Hopkins Institute (USA) in June 2015.
  • ESHG National Fellowship to attend the ESHG annual conference 2012 in Nuemberg, Germany.
  • Distinguished Achievement Medal – Post Graduate Student of the Year (2012) awarded by the Faculty of Medical and Human Sciences, University of Manchester.
  • 2011 Founder’s award for the best presentation at the Skeletal Dysplasia Group Meeting.
  • Dame Barbara Clayton Memorial award for best trainee presentation at British Inherited Metabolic Diseases Group Annual Symposium 2011.
  • Best Presentation at the 2011 Research Showcase of School of Biomedicine, University of Manchester.
  • ESHG Poster Award for an outstanding presentation at the European Society of Human Genetics Conference 2011.
  • Robin Winter Prize for best presentation by a trainee at the 2011 Clinical Genetics Society of UK Annual Spring Conference.
  • Travel Scholarship from Society for the Study of Inborn Errors of metabolism to attend SSIEM 2011 Annual Symposium in Geneva.
  • Travel Bursary from the European Paediatric Neurology Society to attend the EPNS conference 2011, Cavtat.
  • Wellcome Trust Bursary to attend Genomic Disorders 2011 – The Genomics of Rare Diseases Conference, Cambridge.
  • Research Councils UK-India Early Career Researchers’ Travel Funding to attend the Indian Society of Human Genetics Annual Conference 2011, Manipal.
  • British Society of Human Genetics Travel Award to attend Society for Study of Inborn Errors of Metabolism Annual Symposium 2010, Istanbul.
  • Dickinson Trust Travel award for 2008 to attend ESHG course on Genetic Epidemiology in Paris.

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  • SDG 3 - Good Health and Well-being

Areas of expertise

  • RJ101 Child Health. Child health services
  • Rare disorders
  • Developmental disorders
  • Genetic disorders
  • Chromatin disorders
  • chromosomal disorders
  • Kabuki syndrome
  • Copy number variants
  • Non-coding variants
  • Inborn errors of metabolism
  • QH426 Genetics
  • Chromatin
  • Chromosome

Research Beacons, Institutes and Platforms

  • Manchester Regenerative Medicine Network
  • Christabel Pankhurst Institute

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