Mandy Yan Email and Phone Number

• Assay and Algorithm Validation - Validate runs from different instruments (Nextseq550, Nextseq500, Novaseq), extraction/library preparation methods or software parameters. Compare the results between the dev version and production version, i.e. metrics and VCFs.- Test and adjust different machine learning and statistical algorithms (for example: CNV detection, merge variants based on phasing, variant calling) according to products’ goals.• APP and Workflow Development- Develop Applets on DNANexus to meet the in-house pipeline’s requirements.- Create Docker images and WDL files to encapsule the workflows for both germline and somatic analysis; use Git for version control

• Metagenomics- Familiar with different open-sourced classification tools (Blastn, KRAKEN2, Centrifuge etc.) for clinical diagnosis and validation of the results.- Designed and constructed the MySQL database to manage, assess and curate the reference genomes/sequences downloaded from NCBI GenBank. - Detection of AMR genes using RGI and CARD database. - Constructed the automatic mNGS analytical pipeline and utilized Snakemake to manage the pipeline. GitHub was used to control pipeline versions.• Re-sequencing (WGS/WES) - Involved in the work of the semi-automated annotation and classification of BRCA germline mutations in terms of clinical impacts. The progress is inspired by the logic of InterVar and ANNOVAR. - Improved the in-house algorithms to identify the duplicated reads with the UMI tags.

• NGS Analytical Pipeline Construction- Constructed and optimized SNV and INDELs (both somatic and germline) calling pipeline for WES/WGS and panel-based NGS data (tested several tools, including GATK, VarScan, VarDict etc.)• Cancer variants interpretation- Developed a software to interpret the clinical impact of somatic variants (called VIC, results published in the journal “Genome Medicine”. Several databases were utilized in this study, such as ClinVar, COSMIC, CIViC, gnomAD etc.).• Population Genetics- Collaborated with multiple academic institutes and hospitals to discover clinically actionable variants/genes among Chinese populations for certain diseases, such as gastric cancer.

• Comparative Genomics: performed genetic synteny analysis among Rosaceae family using CLC Genomic Workbench and visualize the results with Circos Plot• Diploid Roses Mapping: used the in-house-built pipeline to create the genetic maps for diploid roses (SE reads generated by Illumina 2500, WGS)• Disease Resistant QTL Mapping: combined both phenotype and genotype to perform the association study

TA for Temperate fruits and nuts; and Enology; and Basic horticultural science and practice

Bachelor degree