Genomics midterm 1

Sanger

Gel electrophoresis
very accurate
only need sm amount of DNA

Nanopore

Changes in electrical current idetfy bases
long read length
needs lots of DNA
very fast

Pac Bio

Sequel system
DNA/RNA = isolated
long read
high accuracy
uniform coverage
Single molecule resolution

Illumia Sequencing

Clustered
DNA is copied one base at a time using fluoresce labeled nucleotides
short read length
very acuate
need lots of DNA/lg scale sequencing

HPC

high performance computing

COSMIC

Catalog of somatic mutation in cancer

SNP

Single Nucleotide Polymorphism
High density panel: 777k
med density panel: 50-150k
low density panel: 3-30k
minor allele frequency is 1%

CNV

Copy number variant

INDELS

Insertion/deletion
<1000 bp
DNA = lost or gained

Frameshift mutation

effects reading pattern

Genotype Imputation

converts low - high denisty SNP panel → HD → sequence

Short term value for genomic application

breed comp
genetic inbreeding
Heterozygoty & hybrid vigor
genomic relationship
pedigree correction
sire assignment

GBV

genetic breeding value

EBV

estimate breeding value

PTA

Predicted transmitting ability
½ GBV
used in dairy industry

EPD

Expected progeny difference
½ GBV
used in beef industry

IBD

Identical by decent

QTN

Quantitative trait nucleotide

Structural Genomics

Studying the physical nature of genomes
- includes the sequencing mapping of genomes
- SNP, Indels, CNV (Copy Number Variation in genetics)
- GWAS (Genome-Wide Association Study)

Functional genomics

Expression and function of the entire genome
- transcription
- CHIP - seq
- genome editing
- eQTL & Gene enrichment and Network analyses
- Epigenetics
- Meta-transcripts

Comparative Genomics

Comparing the genomes of different organisms

• detect evolutionary changes across genomes

• Data from ALL species is useful

What factors shaped genomics?

• Advances in Sequencing Technology & reduction in the cost of sequencing

• Computational and Data Science Innovations (e.g.

  Availability of High-performance Computing (HPC)

  Facilities)

• Advances in Data Analytics Approaches such as ML (machine learning)

• Focus shift from a single gene to the genome

Cloud Computing providers

• AWS (amazon web services)

• Google Cloud

• Digital Ocean

• Microsoft Azure

Breadth of coverage

% of bases of a reference genome that are covered with a certain depth

QTL

quantitative trait locus

MAS

Marker assisted selection 1990s

QTL Mapping

moved from single marker association to GWAS/genome wide association **principle remains the same.