Data Training

D. KALPANA

***/** *, **** *****, Second Street, Ponnammapet

Salem, Tamil Nadu, Phone: +91-855-***-****;

Email: **************@*****.***

linkedin.com/in/kalpana-d-3b1004119

Professional Summary

Highly qualified molecular biologist specialized in genomics for more than nine years. Worked on the population genetics and NGS assay validation research projects. Experienced in Next Generation Sequencing (NGS) on the Illumina Miseq, Ion Torrent, Sanger Sequencing and DNA profiling. Having analytical and problem-solving skills and administrative skills. Seeking a challenging technical / research position that will capitalize my skills, education and experience.

Areas of Expertise

• Next Generation Sequencing (NGS) Illumina &

IonTorrent • ddPCR mutation assays for cell free DNA

• RNA extraction-cDNA based qPCR assays • STR/SNP genotyping and Sanger sequencing

• CNV detection qPCR and Translocations assays • Population Genetics and data analysis

• Cancer Panel validation assays & MLPA assays • Serological and Immunological Assays & HLA typing Professional Experience

Integrated Gulf Biosystems, Dubai, UAE Nov 2018 – October 2019 IGB is a market leader for clinical genomic solutions in the Middle East in the Kingdom of Saudi Arabia, United Arab Emirates, Qatar, Bahrain and Libya. Having its own name for the exemplary technical and application Support after sales.

Field Application Specialist:

Working mainly on the technical and application support, technical troubleshoots and product promotions. Thermo Fisher NGS assay applications library prep and technical trouble shoots for Ion Torrent Chef and GeneStudio S5 series platforms.

Sanger sequencing assays for single gene mutation/variant analysis using Seqstudio, ABI3500 and ABI3730 etc.

TaqMan assays for gene expression and SNP detection using ABI7500 and Quantstudio 5, 7 Flux etc STR genotyping training and assay technical trouble shoots for HID and clinical applications. Robotic liquid handling Instruments like ThermoFisher -KingFisher, Pathotrix Auto, Hamilton NGS star and Qiagen & Promega Instruments

GenDX Chimerism qPCR-based assays

FTD qPCR based clinical assays for pathogen detection All other Thermo and other collaborated company products. MedGenome Labs Ltd, Bangalore, India Feb 2018 – Aug 2018 A market leader in genomics-based diagnostics and research from India with global offices in California and CAP accredited NGS lab.

Senior Scientist:

Working mainly on the assay validation, Tech transfer and Quality Management of techniques to expand the Bangalore lab activities.

MLPA assays for Micro/Major deletion

Sanger sequencing assays for single gene mutation/variant analysis Fragment analysis assays for mutation detection and confirmation NGS assay mutation detection and sanger confirmation etc., Maternal Cell Contamination assays

Validation report writing and SOP preparation as per CAP guidance. Strand Life Sciences Pvt Ltd, Bangalore, India May 2014 – Feb 2018 A leader in precision medicine diagnostics aiming to empower cancer care and genomic testing for inherited and rare diseases. India's 1st and only CAP & NABL accredited NGS lab. Senior Scientist 1:

Worked on the different research projects like the ‘Validation of Cell Free DNA (cfDNA) Assay for Liquid Biopsy samples’ and ‘Validation of 152 Somatic Cancer Gene Assay’. In charge of the 152 Somatic Gene panel production samples as well.

• Managing and maintaining of the production samples received for 152 Somatic Gene panel assay.

• Validated the different mutations and gene changes like amplification, deletion and translocation by using qPCR and Sanger sequencing methods.

• Involved in the standardization of the 152 Somatic Gene panel for detecting the somatic mutations at the level of 5% to below 2% in NGS and copy number and translocation (fusion) changes.

• Involved in the Inter/Intra operator/kit etc test for validating the assay.

• Experienced in the various DNA library preparation methods for NGS sequencing

• Limit of Detection (LOD) studies of the custom designed cancer panel on various cell line and Coriell DNA samples for their mutation detection level in the selected gene target sequences, different DNA and library quantization methods.

• Involved in the validating the assay for cfDNA extraction, recovery and mutation detection by ddPCR single gene and multiplex gene assays.

• ddPCR assay confirmation of the mutation find in the NGS data and RNA extraction and cDNA conversion for qPCR assays.

• Standardized an alternative method for FFPE Infinium QC Assay and qPCR-based assay for GC rich regions for confirming mutations.

• Overall Lab Maintenance and supervising the Lab Assistants of the R&D division. Central Forensic Science Laboratory, Kolkata, India Mar 2006-July 2012 Central Forensic Science Laboratory (CFSL), Kolkata, a premier institution of the country working under the Ministry of Home Affairs (MHA) and is the Centre of Excellence in Biological Sciences for R&D. Junior/ Senior Research Fellow:

Worked on the research project named ‘Analysis of Degraded Human DNA by Autosomal Markers with Short Amplicons’. Performed the DNA Extraction, Quantization, Genotyping and Sequencing of STR and SNP markers in the population samples and real samples for population genetic research studies and case reporting.

• Polymorphic 16 mini/midi STR and 52 SNP loci were selected and analyzed in the collected eleven endogamous population samples of India

• Generated the polymorphic autosomal miniSTR & autosomal SNP panels for HID /population Genetic studies

• DNA database had been created for the selected Indian populations

• Worked on the analysis of the real case samples for DNA reporting.

• Trained the Scientific Officers for DNA profiling techniques for human identification.

• Participated in the various national conferences and presented papers. Amity University, New Delhi, India. Nov 2004 – Sep 2005. Amity University is a private research university having multi campuses across the world. It’s well known for its Biotechnology and Business schools.

Lecturer in Forensic Science

Worked as a Lecturer in the Department of Behavioural Health and Allied Sciences to teach B.Sc, M.Sc. and PG Diploma of Forensic Biotechnology students.

• Taught M.Sc., B.Sc. and PG diploma students for basic biological science subjects and DNA technologies.

• Took Special Lectures and practical training classes for the Judges and police professionals for DNA profiling.

• Participated and organized the conferences and workshops conducted in the university.

• Participated in the curriculum and admission processes. Central Forensic Science Laboratory, Chandigarh, India Aug 2004–Oct 2004 Worked under the Lab Systems, Mumbai to assist in the data analysis and reports. Project Assistant

• Assisted in the analysis of data collection, analysis and drafting reports. Amirtha Institute of Medical Sciences (AIMS), Cochin, India Nov 2003- May 2004. The Amrita Institute of Medical Sciences (AIMS) is a super-specialty tertiary care health centre at Kochi, India. Worked with the Department of Analytical Toxicology. Lab Technician

• Worked on the Pilot project named ‘Blood mercury concentration in the fisherman populations.

• Detected blood mercury level in the fisherman population using UV spectrometry and Mercury Analyzer.

• Prepared SOPs for varies assays

Education

Ph.D. in Life Sciences - 2013

Jadavpur University, Kolkata, India

M.Sc. Biotechnology - 2015

Periyar University, Salem, India

M.Sc. in Forensic Sciences (specialized in Biology) - 2003 University of Madras, Tamil Nadu, India

B.Sc. Micro Biology - 2000

University of Madras, Tamil Nadu,

India

Academic Awards / Fellowships:

Senior Research Fellowship(SRF) awarded by the Directorate of Forensic Sciences, India (2008 – 2012) Junior Research Fellowship(JRF) awarded by the Directorate of Forensic Sciences, India (2006 – 2008) Technical Skills

• Bioinformatic: C and PERL programming language, Data Banking and Sequence, Visual Basic and RDBMS, Bowtie and Galaxy etc

• Analysis Software: IonTorrent Server, Ion reporter, Sequencer, Chimer Marker, GeneMapper ID, GeneScan and Genotyper, Sequenom Typer, Powermarker, Genepop, Powerstat, Arlequin, Dispan, Phylip, Structure etc.

• Computer: MS windows, MS Dos, MS Office, power point, excel, Internet etc Publications

• Sen M, Katragadda S, Ravichandran A, Deshpande G, Parulekar M, Nayanala S, Vittal V, Shen W, Phooi Nee Yong M, Jacob J, Parchuru S, Dhanuskodi K, Eyring K, Agrawal P, Agarwal S, Shanmugam A, Gupta S, Vishwanath D, Kumari K, Hariharan AK, Balaji SA, Liang Q, Robolledo B, Gauribidanur Raghavendrachar V, Oomer Farooque M, Buresh CJ, Ramamoorthy P, Bahadur U, Subramanian K, Hariharan R, Veeramachaneni V, Sankaran S and Gupta V.StrandAdvantage test for early-line and advanced-stage treatment decisions in solid tumors.Cancer Med. 2017 May;6(5):883-901. doi: 10.1002/cam4.1037.

• D Kalpana, Tania Ghosh, Sanjukta Mukerjee, Meeta Mukherjee, Anil Kumar sharma, Subhankar Nath, Varsha Rajesh Rathod, Mukesh Kumar Thakar and Ganga Nath Jha Pentaplex Typing of New European Standard Set

(ESS) STR Loci in India Population. Forensic Sci Int. Genet. 2011

• Tania Ghosh, D Kalpana, Sanjukta Mukerjee, Meeta Mukherjee, Anil Kumar Sharma, Subhankar Nath, Varsha Rajesh Rathod, Mukesh Kumar Thakar and Gang Nath Jha . Genetic Diversity of Autosomal STRs in Eleven Populations of India Forensic Sci Int. Genet. (2011) 5: 259–261.

• Sanjukta Mukerjee, Tania Ghosh, D Kalpana, Meeta Mukherjee, Anil Kumar Sharma. Genetic Variation of 10 X Chromosomal STR Loci In Indian Population. Int J Legal Med (2010) 124: 327– 330.

• Sanjukta Mukerjee, Meeta Mukherjee, Tania Ghosh, D. Kalpana, Anil Kumar Sharma. Differential pattern of genetic variability at the DXYS156 locus on homologous regions of X and Y chromosomes in Indian population and its forensic implications. Int J Legal Med (2011) (DOI 10.1007/s00414-011-0646-6).

• Sangeeta Aditya, D Kalpana, Sumita Bhattacherjee, & AK Sharma. Low copy number DNA profiling from Touched fingerprints using miniSTRs- A case study. Indian J Biot. (2011) 10:147-149.

• Tania Ghosh, D Kalpana, Sanjukta Mukerjee, Meeta Mukherjee, Anil Kumar Sharma, Subhankar Nath, Varsha Rajesh Rathod, Mukesh Kumar Thakar and Ganga Nath Jha. Genetic diversity of 17 Y-Short Tandem Repeats in Indian population. Forensic Sci Int. Genet. 2011

• Meeta Mukherjee, Sanjukta Mukerjee, Tania Ghosh, D Kalpana, Neeta Sarkar Roy, Anil kumar Sharma Polymorphisms of four pigmentation genes (SLC45A2, MC1R and TYRP1) among eleven Endogamous Populations of India – Journal of Genetics 04/2013 92(1):135-9

• Sanjukta Mukerjee, Meeta Mukherjee, Tania Ghosh, D Kalpana, Anil Kumar Sharma – Population genetic data for 11 X STR loci in Eleven Populations of India – Legal Medicine, 02 /2012 14(3): 163 – 5

• Sanjukta Mukerjee, Meeta Mukherjee, Tania Ghosh, D Kalpana, Anil Kumar Sharma – Differential Pattern of genetic variability at the DXYS 156 locus on homologous regions of X and Y Chromosomes in Indian Population and its Forensic Implications – Deutsche Zeitschrift fur die Gesamte Gerichtliche Medizin 11 / 2011. Professional Activities

• HID Workflow training (Extraction, Quantitation, CE, GMIDX, NGS, Converge and Rapid DNA)- Thermo Fisher Scientific, Dubai (2018)

• ACT 2015: the 14th Asian Conference on Transcription- National university of Singapore, Singapore

• Next Generation Sequencing (NGS) - Bioinformatics and Data Analysis training -Anna University, Chennai, India (2013)

• ISO / IEC 17025:05 Laboratory Quality, Accreditation Management and Internal Audit training Program - CII, Bangalore, India (2010)

• Training program on Sequenom (iplex) MassArray SNP Genotyping Technology -the Centre for Genomic Application (TCGA), New Delhi, India (2009).

• Forensic Human Identification (HID) workshop in the Lab India (Applied Biosysytems), Gurgoan, India (2007)

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