Dr. Zhao Lai $600,000 NIH Shared Instrument grant

In March 2016, Dr. Zhao Lai was awarded $600,000 NIH Shared Instrument grant (S10 grant 1S10OD021805-01) to purchase Illumina HiSeq 3000 to upgrade the sequencing platform in GSF. Illumina HiSeq 3000/4000(3000 carries one flow cell vs HiSeq 4000 with two flow cell stations) is the latest and most efficient sequencing platform in Illumina NGS market. It provides greater efficiency in terms of high-throughput, faster turn-around-time and cheaper cost. We are very grateful to NIH funding support to continue the GSF’s NGS journey to the new exciting direction.

The enhanced sequencing performance of HiSeq 3000 is enabled by two new technologies: patterned flow cell and kinetic exclusion amplification. These two new technologies were only available on the X Ten sequencers for a single application, the re-sequencing of human genomic samples. In contrast to the random clustering employed previously (HiSeq 2500 and earlier models), the clusters in HiSeq 3000 are now generated in ordered nano-wells to allow for higher cluster densities and unambiguous cluster identification. Unlike Illumina X Ten line dedicated to human genome re-sequencing only, HiSeq 3000/4000 series are capable of processing samples derived from all organisms, making them very flexible and cost-effective sequencing platforms. The decreased cost and the increased capability will significantly benefit every user’s sequencing need and bring the type of genomic analyses once possible only in large-scale sequencing centers to research laboratories both large and small, and make scientific and translational genome sequencing applications closer to reality.

The table below compares with HiSeq 3000 (current) and HiSeq 2000 (previous)

For 50bp single reads sequencing

(most RNA-seq and ChIP-seq)

Instrument

Run time1

# of reads/lane

(millions)

Read Length

(base-pair)

>Q30

Note

HiSeq 3000

(current)

12 hour 300-400 50 90-95% New Chemistry
HiSeq 2000

(previous)

3 days 150-190 50 90-95% V3 Chemistry3

For 100bp paired end sequencing

(most exome-seq and RNA-seq for splicing variants)

Instrument

Run time1

# of reads/lane

(millions)

Read Length

(base-pair)

>Q30

Note

HiSeq 3000

(current)

<2 days 600-800 100 90%-95% New Chemistry
HiSeq 2000

(previous)

11 days 300-380 100 85%-90% V3 Chemistry3

The GSF has purchased HiSeq 3000 in May and installation and training have been completed in June 2016. If you are considering next generation sequencing for your research, please contact Dr. Zhao Lai for consultation on experimental design, pricing and scheduling.

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