Professional Experience

Over a decade of progressive expertise in clinical diagnostics and genomic research

Sep 2019 – Present

Research Associate

Kathmandu Center for Genomics and Research Laboratory (KCGRL), Lalitpur, Nepal

  • Lead genomics projects on rare diseases, prenatal testing, and whole genome analysis
  • Co-authored peer-reviewed publications on human genetics and clinical genomics
  • Organized workshops on NGS technologies and basic bioinformatics
  • Mentored junior scientists in molecular protocols and genomic data analysis
Sep 2019 – May 2025

Molecular Biologist

Nova International Diagnostics, Lalitpur, Nepal

  • Managed NGS workflows including WES and gene panel sequencing for rare and somatic disease diagnostics
  • Executed bioinformatics pipelines for variant calling, annotation, and clinical reporting
  • Designed and validated molecular assays to improve genetic diagnostics efficiency
Aug 2010 – Oct 2019

Medical Laboratory Technologist

Manmohan Memorial Community Hospital, Kathmandu, Nepal

  • Performed diagnostic tests in hematology, microbiology, clinical biochemistry, and pathology
  • Trained and supervised students and junior staff, ensuring laboratory compliance

Technical Expertise

Comprehensive skills across molecular biology, bioinformatics, and clinical laboratory operations

Molecular Techniques

  • Sanger Sequencing
  • Illumina Platform
  • IonTorrent
  • Oxford Nanopore
  • WGS/WES
  • Targeted Panels
  • cfDNA Analysis
  • Germline/Somatic Testing
  • Prenatal Genomics
  • Oncology Genomics
  • Nucleic Acid Extraction
  • PCR/qPCR
  • Library Preparation
  • Electrophoresis

Bioinformatics

  • Targeted Gene Panels
  • WGS/WES Analysis
  • NIPT & PGT
  • Cancer Genomics
  • Germline/Somatic Calling
  • CNV/SV Detection
  • Mutational Signatures
  • Genome Assembly
  • AMR Profiling
  • GATK
  • bcftools
  • samtools
  • VEP
  • IGV
  • Nextflow
  • Cromwell
  • Cloud Pipelines

Clinical Laboratory

  • Hematology Diagnostics
  • Microbiology
  • Clinical Biochemistry
  • Pathology
  • Molecular Assays
  • ISO 15189 Compliance
  • GCLP
  • SOP Development
  • Internal Audits
  • QA/QC Management

Programming & Data

  • Linux
  • Bash Scripting
  • Python (Intermediate)
  • R (Basic)
  • Workflow Automation
  • Data Processing
  • Cloud Deployment

Research Contributions

Peer-reviewed publications, books, and conference abstracts in genomics and diagnostics

Non-invasive prenatal testing (NIPT) by DNA sequencing method

Sandeep Thapa, Nilam Thakur, Govardhan Joshi, Santosh Khanal, et al.

EC Gynaecology 2024
Read Publication

Phytochemical analysis of medicinal plants of Nepal and their antibacterial activities

Sudip Bhandari, Karan Khadayat, Santosh Khanal, Bishnu P. Marasini, et al.

BMC Complementary Medicine and Therapies 2021
Read Publication

Rare pathogen Pseudomonas stutzeri: A case report from Nepal

Joshi Govardhan, Sakrita Hona, Santosh Khanal, Pooja Maharjan, et al.

Int. J. Medicine & Biomedical Sciences 2018
Read Publication

Epidemiological analysis of dengue: A review

Bishnu P. Marasini, Sudip Bhandari, Santosh Khanal, Sunil Shrestha

Int. J. Medicine & Biomedical Sciences 2018
Read Publication

Practical Manual of Medical Laboratory Technology (1st ed.)

Santosh Khanal, Sweeti Upadhaya, & Bharat Pathak

Samiksha Publication (ISBN 978-9937-792-68-4) 2025
View Book

Establishment of Nepal’s First NIPT Service Laboratory

Santosh Khanal et al.

ASHG Conference Poster PB2070 2023
View Abstract

Education & Certifications

Academic background and professional training in biotechnology and diagnostics

M.Sc. in Biotechnology

Tribhuvan University, Nepal

2016 – 2020

Thesis: Non-Invasive Prenatal Diagnosis from Maternal Cell-Free Fetal DNA: Ion Semiconductor Sequencing Validation and Clinical Performance

B.Sc. in Medical Laboratory Technology

HNB Garhwal University, India

2005 – 2008

Higher Secondary Education (Science)

HSEB, Nepal

2003 – 2005

Professional Trainings

Cancer Genome Analysis - Asia

Wellcome Connecting Science & Khon Kaen University

October 2025

NGS Bioinformatics Essentials

Oxford University Clinical Research Unit (OUCRU), Nepal

December 2024

SeqStudio Genetic Analyzer Training

Thermo Fisher Scientific, India

March 2024

Pathogen Genomics Workshop

Doherty Institute & CMDN, Nepal

January 2023

Ion OneTouch and Ion S5 Training

Thermo Fisher Scientific, India

August 2019

Let's Connect

Get in touch for collaborations, research opportunities, or consulting

Location

Kathmandu, Nepal

Phone

+977 9851068856

Email

ask.san@gmail.com