BALA SUBRAMANI GATTU LINGA
Bioinformatics Scienitst
Abu Dhabi
Summary
Molecular biologist and Bioinformatics scientist with 7 years with practical experience in molecular biology, molecular genetics, computational genomics, and NGS techniques. Skilled in developing and implementing computational methods, and workflows to analyze high throughput omics data.
- Experience in handling and analyzing NGS sequencing data - finding genetic variants, CNV, SNV, and Indel from Clinical exome, focused exome, and Whole-exome sequencing samples. Experience in defining innovative analysis strategies, from raw data to biological interpretation. Holding experience in NGS and microarray data analysis, single-cell data analysis, data management, pipeline management, annotation, and visualization.
- Skilled in with python libraries (Pandas, NumPy, SciPy, TensorFlow, Matplotlib, Seaborn and Keras) and statistical tools such as PCA, clustering, and Regression analysis. and Shell scripting.
- Competent working in Linux environments and HPC/cloud computing.
My research and career interest lies in understanding the composition of the human genome for studies of genetic disease built around three themes:
1. Gene copy number and structural variation in the human genome.
2. Determining the genetic architecture in Pediatrics/Developmental disorders, metabolic and neurology disorders.
3. Developing bioinformatics infrastructure and pipeline workflow-analysis for clinical genomics data and translational genomics research.
Overview
10
10
years of professional experience
10
10
years of post-secondary education
15
15
Certificates
4
4
Languages
Work History
Bioinformatician
National Reference Laboratory
Abu Dhabi
09.2022 - Current
- Working as Bioinformatician (from September 2022 – Till Date), Molecular Diagnostics and Genomics Laboratory, National Reference Laboratory, Abu Dhabi, UAE.
- Integral developer of the computational/analytic tools associated with new high-throughput genetic technologies under development.
- Design, implement, and test novel and reproducible NGS analysis methods/ workflows and also to design custom scripts to support the analysis of high-throughput data.
- Develops and implement new QC measures and algorithms into the pipelines, processes or analyses and assures quality control criteria are met, and clinical cases are reported timely.
- Performs statistical and integrative data analysis of genomic data, summarizing complex datasets, and presenting analysis results in professional/concise manner.
- Assists with the development of standard operating procedures for bioinformatics analysis of clinical tests
- Performs data management, data analysis and other bioinformatics-related tasks in coordination with other genomics staff.
- Building and maintaining Bioinformatics pipelines in a CAP/CLIA clinical environment and ensure it compliance.
- Utilize statistical and machine learning techniques to aid in the interpretation of quantitative genomic data.
- Maintains and implements changes to lab informatics systems and other software interfaces as needed.
- Work in conjunction with wet lab and tech teams to ensure smooth operations and development work.
- Serve as a technical expert in bioinformatics within the organization and provide support to multiple projects and programs.
- Work closely with colleagues in NRL to help ensure alignment of research-based bioinformatics activities with clinical bioinformatics, direction where appropriate.
- Resolved problems, improved operations and provided exceptional service.
Bioinformatics Scientist - Consultant
Centogene GmbH
Rostock
04.2022 - 07.2022
- Worked as Bioinformatics Scientist - Consultant (April 2022 – July 2022), Clinical Bioinformatics, Clinical Lab operations, Centogene GmbH, Rostock, Germany.
- Experience working with Centogene in-house software for tertiary analysis of NGS data to filter to narrow down clinically relevant variants.
- Hands-on application of software tools and databases for genomic interpretation.
- Analyzing and interpreting clinical cases (clinical genomics data generated from Illumina’s NGS technology) using various NGS panels/backbones such as WES, WGS, and CentoDx.
- SNP, CNV and SV detection, verification and troubleshooting for the interpretation team.
- Experience in solving/analyzing tricky and borderline cases using WES and WES backbone of NGS.
- Database navigation (e.g. ClinVar, Varsome, OMIM, Ensembl VEP, SnpEff, SnpSift, HGVS, gnomAD, HGMD, etc.) and thorough literature review to collect evidence for identifying variants overlapping with clinical phenotype.
- Close collaboration with medical bioinformatics and the reporting team for effective interpretation of borderline clinical cases.
- Analyzed problematic areas to provide recommendations and solutions.
- Organized and analyzed primary and secondary research to understand industry, market and company trends.
Team Leader/Assistant Manager – Molecular Genetics
Lifecell International Pvt. Ltd.,
Chennai
12.2020 - 04.2022
- Tertiary analysis of NGS data from a wide spectrum of clinical samples. Analyzed over 1500 Exome datasets with suspected genetic aetiology. Experience in germ-line genetic variant interpretation of over 1000s variants. The area of interest is rare genetic disorders (monogenetic, multifactorial inherited disease, chromosomal disorders), by analyzing exome level NGS (Illumina paired-end technology) data. Also, involved in the management and establishment of bioinformatics infrastructure for analyzing patient-specific genomic datasets for diagnostic/research purposes.
- Worked as a team player in the Clinical Bioinformatics/Analysis team and performed NGS data analysis and interpretation of variants/mutations causing genetic disorders using standard guidelines.
- Worked with Illumina’s Miseq, NextSeq and NovoSeq platforms to analyze DNA-seq data.
- Thoroughly worked on Golden Helix – Varseq (a commercial software) for understanding, processing, and analyzing the clinical NGS data to identify disease-causing genetic variants.
- NGS data analysis and interpretation of variants/mutations causing genetic disorders using standard guidelines.
- Interpreting NGS-based (whole exome sequencing, whole genome sequencing) results, for the purpose of diagnostic testing and/or risk screening.
- Experience in establishing real-world evidence-based clinical and scientific correlations, applying genetic & genomic routines, and complex laboratory tests.
- Experience in working with ACMG-recommended variant classification guidelines and creation of high-quality variant interpretation reports.
- Worked on automation, standardization, maintenance, and protocol development for inherited and rare disease diagnostics.
- Well-versed with custom panel design, Data Analysis and Quality control checks for the NGS platform and developing SOP for interpretation of NGS-based results.
- Assist in creating and implementing the NGS data analysis pipeline for automation and faster report generation.
- Close interaction with clinical collaborators to obtain additional information required to diagnose cases and to confirm new candidate variants and genes.
- Supporting Laboratory Genetic Counselors and inside/external sales to respond to client requests for information on the interpretation/classification of individual variants.
- Built strong relationships with customers through positive attitude and attentive response.
- Mentored and guided employees to foster proper completion of assigned duties.
- Implemented new working processes to deliver multiple improvements.
Bioinformatician
Genestrings Diagnostic Centre Pvt. Ltd.,
New Delhi
03.2020 - 12.2020
- Skilled in preimplantation genetic screening from embryo biopsy by Next Generation
- Sequencing (NGS) as part of diagnostic services for patients undergoing in vitro fertilization.
- Experience in performing PGT-A, PGT-M and PGT-SR.
- Experience in performing Non-invasive prenatal testing (NIPT) algorithms to detect chromosomal anomalies.
- Detection of the germ-line mutation using the multigene-targeted SNP panels.
- Experience in identifying structural variants in various neurodevelopmental disorders (Autism, Parkinson’s’ disorder, etc.,).
- Expertise in processing NGS data in Ion Torrent technology pipelines such as Ion torrentsuite and Ion reporter.
- Gained experience in COVID-19 diagnosis, data analysis, interpretation, and report preparation using Real-Time PCR and immunoassays.
- Experience in setting up of lab infrastructure, calibration and validation of lab equipment, and standardization of lab techniques.
- Used critical thinking to break down problems, evaluate solutions and make decisions.
Senior Research Fellow (ICMR)
School of Biotechnology (SBT), Jawaharlal Nehru University
New Delhi
03.2016 - 03.2019
- Completed ICMR-SRF (March 2016 - March 2019) research project entitled “Structural, mechanistic and functional dynamics studies on putative TetR family transcription regulators from Mycobacterium tuberculosis using computational and biophysical techniques (Mtb)”.
- Leveraged various computational (Molecular Dynamics, Molecular mechanics, Structural bioinformatics) and molecular biology techniques (Protein purification and biochemical assays) to elucidate transcriptional regulatory mechanism in Mtb.
- Prepared variety of different written communications, reports and documents.
- Exceeded goals through effective task prioritization and great work ethic.
- Maintained energy and enthusiasm in fast-paced environment.
Skills: Linux · Shell Scripting · Algorithms · Structural Genomics · Molecular Biology · Bioinformatics · Machine Learning · Drug Discovery · Structural Biology · Structural Bioinformatics · Molecular Dynamics · Molecular Medicine
Junior Research Fellow (DST)
Institute of Microbial Technology (CSIR)
Chandigarh
07.2013 - 01.2015
- Worked on DST-sponsored project entitled “Design and Development of Promiscuous peptide inhibitors for metallo-
aminopeptidases” - Leveraged computational and molecular techniques such as molecular mechanics, molecular dynamics and X-ray crystallography to deduce molecular promiscuity in metallo-peptidases.
- Developed bioinformatics tools and python programming scripts to calculate structural parameters of various metallo-peptidases.
- Conducted research, gathered information from multiple sources and presented results.
- Delivered services to customer locations within specific timeframes.
Skills: Linux · Statistical Data Analysis · Shell Scripting · Structural Genomics · Bioinformatics · Drug Discovery · MATLAB · Structural Biology · Structural Bioinformatics · Molecular Dynamics
Project Assistant Level-II
Institute of Microbial Technology (CSIR)
Chandigarh
07.2011 - 06.2013
- Worked onDBT-sponsored project entitled “Assembly, Structure & Regulatory Mechanism of transcriptional regulatory complexes (TRCs) of Salmonella typhimurium”
- Leveraged computational and molecular techniques such as molecular mechanics, molecular dynamics and X-ray crystallography to deduce transcriptional regulatory mechanism in Salmonella typhimurium.
- Unravel the structural mechanism of cysteine synthase complex using molecular dynamics simulations.
- Conducted research, gathered information from multiple sources and presented results.
- Delivered bioinformatics services to research projects within specific timeframes.
- Participated in continuous improvement by generating suggestions, engaging in problem-solving activities to support teamwork.
- Led projects and analyzed data to identify opportunities for improvement.
Skills: Linux · Statistical Data Analysis · Shell Scripting · Structural Genomics · Bioinformatics · Drug Discovery · MATLAB · Structural Biology · Structural Bioinformatics · Molecular Dynamics
Research Trainee (DBT)
Madras Christian College (Autonomous)
Chennai
08.2010 - 06.2011
- Completed a project on MICROARRAY (Gene expression analysis) entitled “Gene expression analysis of rheumatoid arthritis and its response to various drug entities”
- Completed a project entitled “Homology Modeling, Docking and structural analysis of Hemagglutinin - Neuraminidase using Sialic Acid Inhibitor”
- Conducting Biotechnology and Bioinformatics practical classes to post graduate students.
- Guided post graduate students for their dissertation projects
- Created spreadsheets using Microsoft Excel for daily, weekly and monthly reporting.
- Developed e-learning modules and portals for bioinformatics virtual classroom.
Education
Ph.D. - Biotechnology
Jawaharlal Nehru University
New Delhi 01.2015 - 12.2019
Master of Science - Bioinformatics
Sri Ramachandra Medical University
Chennai 07.2007 - 07.2009
Bachelor of Science - Microbiology
University of Madras
Chennai 06.2004 - 05.2007
Skills
Teamwork and Collaboration
Certification
Sun Certified JAVA Programmer - Sun Microsystems (Dec 2009)
Accomplishments
ICMR Senior Research Fellowship - Indian Council of Medical Research, New Delhi (2016-2019).
CSIR Travel Award - To present research paper in Gordon Research Conference, USA (Aug 2018).
ICMR Travel Award - To present research paper in Gordon Research Conference, USA (Aug 2018).
Young Scientist and Best Poster Presentation Award - NCAAE-2018, Jamia Hamdard, New Delhi, India (Nov 2018).
EMBO Travel Award - “Pathogen immunity and Signaling”, EMBO Workshop, Oxford, United Kingdom (Apr 2019).
ICGEB Fellowship Award - “Nuclear and Cytoplasmic Molecular Machines at Work”, NYU Abu Dhabi campus, United Arab Emirates (Apr 2019).
EMBO Travel Award - “Chromatin and Epigenetics”, EMBO Workshop, EMBL Heidelberg, Germany (May 2019).
ICGEB Fellowship Award - “High Content Imaging and Data Science for Virtual Screening and Drug Discovery", ICGEB-TRAIN Workshop Bled, Slovenia (May 2019).
Best Poster Presentation Award - “ICBTM-2019”, University of Delhi, Loyola University Chicago & Stritch School of Medicine, USA (25th - 26th Feb 2019).
ICGEB Fellowship Award - “Epigenetics of infectious and non-communicable diseases”, Cape Town, South Africa (Sep 2019).
BioExcel Travel Award - “Structural Bioinformatics”, EMBL-EBI training course on Cambridge, United Kingdom (Sep 2019).
EMBO Travel Award - “DNA topology and topoisomerases in genome dynamics”, EMBO Workshop, Les Diablerets, Switzerland (Sep 2019).
Student/ECR Travel Award - “18th Human Proteome Organization World Congress HUPO 2019”, Adelaide, Australia (Sep 2019).
NGBT GYAN Scholarship Award - “Nextgen Genomics, Biology, Bioinformatics and Technologies Conference (NGBT-2019)”, Mumbai, India (Sep - Oct 2019).
EMBO Travel Award - “The impact of bacterial infections on human cancer”, EMBO Workshop, Berlin, Germany (Oct 2019).
EMBO Travel Award - “Histone chaperones: Structure, function and role in development and disease”, EMBO Workshop, Crete, Greece (Oct 2019).
Sun Life Sciences Pharma Award for Best Poster of young scientist - Society of Neurochemistry, India (Dec 2019).
Best Oral Presentation Award - “International Conference on Biology in 21st Century: Transformation of Biological Sciences in Supporting the Sustainable Developmental Goals”, - Indian Science Congress Association, India.
Best Oral Presentation and ACS journal award - “Chemical Science for Drug Discovery & Therapy” - Visvesvaraya National Institute of Technology (NIT), Nagpur, India (Jul 2020).
Best Poster Presentation Award - “Emerging Trends in Health and Disease Research”, Amity University, India (Oct 2020).
Young Scientist and Best Poster Presentation Award - “International Conference on Engineering, Medical, Biomedical and Biological Sciences (IVCEMBBS 2020)” - SynBiogenica Labs, India (Oct 2020).
Best Oral Presentation Award - “International Symposium on Bioinformatics and Artificial Intelligence in Covid-19 era and beyond”, Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India (Nov 2020).
Best Oral Presentation Award - “Virtual International Conference on - Recent Advances in Chemical and Biological Science” (ViRACBS-2020), Dayananda Sagar College of Engineering (DSCE), Bangalore, India (Dec 2020).
Best Poster Presentation award - “BioSangam 2022: Emerging trends in Biotechnology”, National Institute of Technology, Allahabad (March 2022).
Young Investigator Award - “Genomic Medicine Short Course”, Children’s Mercy, Kansas City, Missouri, United States (June 2022).
Admirable Scientist Award - International Scientist Awards on Engineering, Science and Medicine (INSO), India (June 2022).
Editorial Board Member - Computational Biology and Bioinformatics, SciencePG (Science Publishing Group).
Workshops and Trainings
“Molecular Modeling & Simulation (Accelrys)” - Sai Biosciences Pvt. Ltd., (Accelrys) Chennai, India (June 2008).
“Schrodinger Software for Biological and Material Science Application Workshop” -Jawaharlal Nehru University (JNU), New Delhi, India, (Jul 2016).
“Transmission Electron Microscopy for Material Science Workshop”, - Jawaharlal Nehru University (JNU), New Delhi, India (Nov 2016).
“Field Emission Scanning Electron Microscopy based Lithography Workshop” - Jawaharlal Nehru University (JNU) & TESCAN Orsay Holding, A. S., Czech Republic, (May 2017).
“Time-Resolved Fluorescence Spectroscopy (TRFS) Femtosecond Fluorescence up-conversion and their research applications workshop”, - Jawaharlal Nehru University (JNU), New Delhi, India (Oct 2017).
“Combined Confocal Raman - AFM System and its Research Applications workshop”, - Jawaharlal Nehru University (JNU), New Delhi, India (Aug 2018).
“Advancement in Flow Cytometry Technology and Its Application in Research workshop”, - Jawaharlal Nehru University (JNU) & Thermo Fisher Scientific (Jun 2019).
“Advanced Spectroscopy Techniques for FTIR and FTNIR workshop” - Jawaharlal Nehru University (JNU) & Perkin Elmer (Jul 2019).
“Artificial Intelligence: Concepts and Multidisciplinary Applications in Modern Biology workshop” - Apex-BTIC, ICGEB, New Delhi (Sep 2019).
“Comprehensive Workflow of Real-Time PCR workshop” - Genestrings Diagnostic Centre Pvt. Ltd., New Delhi (Aug 2020).
“Recent Advances in Artificial Intelligence-Training Program” - TEQIP-III and National Institute of Technology (NIT), Uttarakhand (Jul 2020).
“Recent Advances in Nest Generation Sequencing (NGS)-Faculty development program” - Centre for Ocean Research, Ministry of Earth Sciences - Earth Science Technology Cell (MoES- ESTC) (July - Aug 2020).
“R-programming & its application in Biomedical Research workshop” - Indian Institute of Technology-Delhi (IIIT-D) (Aug 2020).
“ADVIA Centaur® XP Immunoassay System - Training Course” - Siemens Healthineers, Germany (Aug 2020).
“6th National Conference on Indian Society of Inborn Errors of Metabolism conference” - Indian Society of Inborn Errors of Metabolism and Institute of human genetics (Aug 2021).
“Computational Biology and Network Pharmacology: New Horizon in Drug Discovery Workshop” - Department of Pharmaceutical Sciences and Drug Research Punjabi University, Patiala, Panjab (Dec 2021).
"Recent Updates on Nutrition: Focus on Metabolic Disorders - Faculty Development Program" - Sathyabama Institute of Science and Technology, Chennai, (Jan 2022).
“Data Analysis using R Commander workshop” - Global Institute of Statistical Solutions (Feb 2022).
“Medical Image and Signal Processing using Python - MIS2P’22 Workshop” - Sasi Institute of Technology and Engineering, A.P., India (Mar 2022).
“Natural Language Processing - Faculty Development Program” - IIT Kanpur, IIT Roorkee, MNIT Jaipur, NIT Patna and PDPM IIITDM Jabalpur, (Feb 2022).
“DNA Decoded” - McMaster University (Mar 2022).
“From Disease to Genes and Back” - Novosibirsk State University (April 2022).
“Whole-genome sequencing of bacterial genomes - Tools and applications” - Technical University of Denmark (Mar 2022).
“CRISPR Advanced” - Biotecnika Info Labs Pvt. Ltd., Bangalore, India (April 2022).
“Artificial Intelligence in Biology” - Biotecnika Info Labs Pvt. Ltd., Bangalore, India (April 2022).
“Precision Medicine” - Biotecnika Info Labs Pvt. Ltd., Bangalore, India (April 2022).
“Vaccine Design & Development” - Biotecnika Info Labs Pvt. Ltd., Bangalore, India (April 2022).
“Next Generation Sequencing” - Biotecnika Info Labs Pvt. Ltd., Bangalore, India (April 2022).
“Stem Cell Technology” - Biotecnika Info Labs Pvt. Ltd., Bangalore, India (April 2022).
“Precision Medicine for Your Practice: Exome Testing for Diagnosis Course” - American Medical Association (March 2022).
“Genomics for Law” - University of Illinois at Urbana-Champaign (May 2022).
“Precision Medicine” - University of Geneva, Switzerland (May 2022).
“Drug Discovery” - University of California San Diego (July 2022).
Oral and Poster Presentation
Oral Presentation “Recent Advances in Biological Research(RABR-2020)” - Heredity Lifesciences (Aug 2020).
Oral presentation "International Conference on Biomacromolecules and Cellular Interface (ICBCI-2021)" - Dr B. R. Ambedkar National Institute of Technology Jalandhar, Punjab, India (Jan 2021).
Oral presentation “1st International Congress of Gerontology” - İKSAD- Institute of Economic Development and Social Research Gerontology Studies Application and Research Center, Turkey (Mar 2022).
Oral presentation “International Symposium on Current Developments in Science, Technology and Social Sciences” - BILTEK Congress, Turkey (Sep 2022).
Oral presentation “International Modern Scientific Research Congress -III” - Istanbul Gedik University, Istanbul, Turkey (May 2022).
Oral and technical Presentation “4th International Conference of Food, Agriculture and Veterinary Sciences” - Van University, Turkey (May 2022).
Oral presentation “2nd International Colloquium on Infectious diseases, Epidemiology and Public Health - ICIEP 2022” - Lumiminds Conventions, Amsterdam, Netherlands (Sep, 2022).
Oral and technical presentation “International Congress on Natural & Medical Sciences” - Ege University, Izmir, Turkey (Sep 2022).
Poster presentation “International Conference on Biomolecular simulation and Dynamics”, - Department of Biotechnology, Indian Institute of Technology (IIT-Madras), India (Nov 2013).
Poster presentation “National Workshop on Fluorescence and Raman Spectroscopy - FCS2018”, - Jawaharlal Nehru University (JNU) and Indian Institute of Technology-Delhi (IIT Delhi), India (Nov 2018).
Poster presentation “59th Annual Conference of Association of Microbiologists of India- AMI 2018 - International Symposium on Host-Pathogen Interactions” - University of Hyderabad, India (Dec 2018).
Poster presentation “Biological Transactions: From Molecules to Organisms (BTMO)” - Indian Institute of Science (IISc), India (Jan 2019).
Poster presentation “Combat-HIV International Conference On “Biology And Therapeutics of HIV & Associated Infections” - University of Hyderabad and Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India, (Jan 2019).
Poster presentation “Conference on Magnetic Resonance in Medicine and 25th National Magnetic Resonance Society Meeting” - All India Institute Of Medical Sciences (AIIMS), New Delhi, India (Feb 2019).
Poster presentation “Regulatory epigenomics: From large data to useful models” - European Molecular Biology Organization (EMBO) & The Institute of Mathematical Sciences, Chennai, India (Mar 2019).
Poster presentation “9th International Meeting on NextGen Genomics, Biology, Bioinformatics and Technologies (NGBT) Conference” - SciGenom Research Foundation (SGRF), Mumbai, India (Oct 2019).
Poster presentation “Calcium Signalling: Molecular mechanisms to a role in health and diseases” - European Molecular Biology Organization (EMBO) & National Centre for Biological Sciences (NCBS), Bangalore, India (Jan 2020).
Poster presentation “Biotechnology and Bioinformatics Research in Healthcare: Why and How?” - Centre for Health Science and Technology (CHeST), JIS Institute of Advanced Studies & Research, Kolkata (Feb 2022).
Timeline
AWS Fundamentals Certification
01-2023
Digital Product Management Certification
01-2023
Prepare Data for Exploration Certification
01-2023
DevOps on AWS Certification
12-2022
IBM AI Foundations for Business Certification
10-2022
Bioinformatician
National Reference Laboratory
09.2022 - Current
Scrum Master Certification
09-2022
AI in Healthcare Certification
08-2022
Agile Meets Design Thinking
08-2022
Data Visualization with Tableau Certification
08-2022
Java Programming and Software Engineering Fundamentals Certification
08-2022
Agile Development Certification
08-2022
Core Java Certification
08-2022
Bioinformatics Scientist - Consultant
Centogene GmbH
04.2022 - 07.2022
IBM Data Science Professional Certification
05-2021
Team Leader/Assistant Manager – Molecular Genetics
Lifecell International Pvt. Ltd.,
12.2020 - 04.2022
Genomic Data Science Certification
11-2020
Bioinformatician
Genestrings Diagnostic Centre Pvt. Ltd.,
03.2020 - 12.2020
Senior Research Fellow (ICMR)
School of Biotechnology (SBT), Jawaharlal Nehru University
03.2016 - 03.2019
Ph.D. - Biotechnology
Jawaharlal Nehru University
01.2015 - 12.2019
Junior Research Fellow (DST)
Institute of Microbial Technology (CSIR)
07.2013 - 01.2015
Project Assistant Level-II
Institute of Microbial Technology (CSIR)
07.2011 - 06.2013
Research Trainee (DBT)
Madras Christian College (Autonomous)
08.2010 - 06.2011
Sun Certified JAVA Programmer - Sun Microsystems (Dec 2009)
12-2009
Master of Science - Bioinformatics
Sri Ramachandra Medical University
07.2007 - 07.2009
Bachelor of Science - Microbiology
University of Madras
06.2004 - 05.2007
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