Genome / Exome sequencing

Whole Genome Sequencing (WGS)

Whole genome (re)sequencing (WGS) is a method to analyze a specific polymorphism from a species with a known reference genome.  It provides the most comprehensive map of an organism’s genetic make-up. The method can discover molecular sarcoma and various genetic polymorphisms (SNPs, insertions, deletions, inversions, complex rearrangements, copy number variation) related to performance and other useful applications. Unlike targeted or exome sequencing, WGS covers all corners of an organisms’ entire genome, which is arguably the most important molecular data. For bacteria, this approach is highly effective for studying virulence, drug resistance or novel drug targets. Similarly, comparative genomic for eukaryotes through resequencing or de novo assembly is the best approach to obtain high resolution genomic variations.

 

For whole-genome sequencing, the combination of short inserts and longer reads allow characterization of any genome. For de novo whole-genome sequencing, the unparalleled raw read accuracy of Pacific Bioscience’s next-generation sequencing (NGS) technology provides high quality, long contig assemblies.

 

Key features for DNA Link Sequencing Lab’s WGS service
Sequencing Platform Illumina, PacBio
Starting Material  more than 3ug of gDNA (or raw material enough to extract equivalent amount of gDNA)

over 40ng/ul of concentration

OD260/280 = 1.8-2.0

Run Mode 125PE, 150PE for illumina

SMRTcells for Sequel or RSII from PacBio

Read depth 30X for human with illumina

50-100X for de novo for plant/animal by PacBio

Bioinformatics Analyses Read alignment
SNP and Indel calling
de novo assembly*
Unified genomic variation detection
Turn-around Time 2-4 weeks for sequencing plus 2-3 weeks for analysis
Data Storage 6 months

 

Whole Exome Sequencing (WES)

Exome Sequencing is a method that selectively analyzes only coding region (Exon), which composes 1-2% of the genome. It is a cheaper and effective way of sequencing compared to whole genome sequencing that analyzes the entire genome.  The iterative detailing of the data amassed from exome sequencing can be very resourceful for teasing out, with high precision and reliability, single-nucleotide variants and de novo mutations associated with both Mendelian and common diseases. Based on these analysis results, exome sequencing can be effectively used in research for rare disease, cancer genomics, and genetic disorders.

 

Exome Capture method

DNA Link Sequencing Lab uses various Exome Capture kits to provide Exome sequencing service.

Agilent SureSelect
illumina Nextera Rapid (Expanded)
Ion AmpliSeq Exom
Method
Solution Hybridization
Hybridization
Targeted PCR
Target size
50M~75M(V3~V5+UTR)
37M (62M)
33M(~58M)
Contents
Exons(+UTR)
Exons(Exons, UTR, miRNA)
Exons
Library Design Time
3days
1.5days
6hrs
Input DNA
1ug (3ug)
50ng
50~100ng
Sequencer
Hiseq 2500
Ion Proton / S5 system

Experiment Work Flow

platform
protocol
Sample Type
minimum Concentration
minimum volume
Required Amount (including QC)
HiSeq
SureSelect exome
gDNA
25ng/ul(3ug) or 8.4ng/ul(1ug)
120ul
4ug or 2ug
HiSeq
Truseq exome
gDNA
20ng/ul
55ul
2ug
HiSeq
Nextera Rapid Capture Exome
gDNA
5ng/ul
10ul
500ng
HiSeq
Nextera Rapid Capture Expanded Exome
gDNA
5ng/ul
10ul
500ng
Proton
SureSelect(modify)
gDNA
8.4 ng/μL
120ul
2ug
Proton
LT exome
gDNA
8.4 ng/μL
120ul
2ug
Proton
AmpliSeq Exome
gDNA
4.8ng/ul
21ul
1ug

Turnaround time

platform
Illumina HiSeq / Agilent SureSelect
Ion ProtonTM & S5 Ion AmpliSeq Exome
Run Info
2×100 Paird End
Ion PITM / Ion 540 Chip(v3)
Time for Experiment * Based on production of raw data
6 weeks
2 weeks

* The time is based on the production of raw data, and may be adjusted depending on the number of samples.