clinical sequencing

Sample Prep for Clinical Sequencing with Sami Amr, Partners Center


Sami Amr, PhD, Director of the Sequencing Core, Partners HealthCare Center for Personalized Genetic Medicine (PCPGM)

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Listen (8:30) How is NGS sample prep improving in clinical applications?

Listen (3:22) Will we get to a one-touch system?

Listen (5:12) Panel or exome?

Listen (4:12) Lab tech proficiency

To finish up our NGS 2014 series, we're joined by Sami Amr, Director of the Sequencing Core at Harvard's Partners Center. Sami and his colleagues are using NGS for ever more clinical applications. How must sample prep improve as genomics goes clinical? Will we ever get to a one-touch system? Which sequencing platform does Sami prefer? These are some of the questions the hands-on lab director addresses in today's interview.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.

Stefan Roever Talks the Future of Next Gen Sequencing


Stefan Roever, CEO, Genia

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Listen (7:34) Update on Genia technology

Listen (3:31) How will you compete with Illumina?

Listen (7:52) How will genomics scale in the clinic?

Listen (3:52) Encouraged to see nanopore sequencing now go commercial

Listen (3:26) Archaic regulatory environment holding back genomic medicine

Listen (5:10) Are you a believer in the DTC space?

Stefan Rover is the CEO of Genia Technologies, where he and his team are working on the next NGS technology. This space has become dominated by Illumina, who this year announced they had achieved the important benchmark of the "$1,000 genome." Stefan and Genia aim for the "$100 genome." In today's interview, we ask Stefan just what it will take for a new technology to break in to the sequencing market.

Beginning with an update on Genia's nanopore based sequencing, Stefan then goes on to talk about how NGS will scale in the clinic.

"Ultimately you don't want a doctor or the clinic to worry about how much does the instrument cost, how many reagents to order, and at what cost, etc," says Stefan. "All they want to do is provide a test and get an answer. And handling things like analysis in the cloud, or patient confidentiality, or integration with payer reimbursement systems---all of that is something that can be handled in a cloud service that can be integrated with the instrument."

Stefan says that the biggest challenge for genomic medicine is our regulatory system, which he calls "archaic." Speaking directly about the FDA's recent clamp down on 23andMe, he favors a system where there are competing regulatory agencies and where the market itself is allowed to raise the value of genomic tests.

Stefan says he's "absolutely" a believer in the DTC genomics space. Consumers own their genomic data and should be able to access it freely, he contends.

"The consumer should be able to go to any service they want and ask any question they want regarding their data."

The discussion about regulation with Stefan provides a preview into our upcoming series, Regulation and Genomic Medicine, where we'll be interviewing Cliff Reid of Complete Genomics, Anne Wojcicki of 23andMe, Alberto Gutierrez of the FDA, among others.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.

The Clinical Sequencer

A Feburary 7th article in the online version of Nature magazine began with the line, "Genomics finally came of age as a clinical discipline on November 19, 2013, when the US Food and Drug Administration (FDA) approved Illumina's MiSeqDx next-generation sequencing (NGS) system for clinical use."   

Now, some may argue with this and say genomics was coming of age with the BRCA test from Myriad back in the nineties, or with the use of NGS for cancer treatment, or the rise of prenatal diagnostics.

A New Gold Standard for Accuracy in NGS: Mike Hunkapiller, PacBio


Mike Hunkapiller, CEO, Pacific Biosciences

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Listen (4:58) What is the theme for 2014 at PacBio?

Listen (2:50) Are you working on a clinical sequencer?

Listen (6:55) What are your thoughts on regulation and diagnostics?

Listen (3:12) What was your reaction to the Oxford Nanopore data just released at AGBT?

Listen (6:40) PacBio runs becoming the gold standard in microbial sequencing

Mike Hunkapiller, the CEO of Pacific Biosciences, joins us again this year as part of our annual series on NGS. Last year, Mike stressed the importance of PacBio's SMRT(TM) sequencing to do longer reads than the competition--namely Illumina. He says PacBio will continue to stay focused on further improving read length and accuracy this year as well. In fact, he says that the PacBio technology is becoming "the new gold standard" for microbial sequencing.

What does Mike think of the first data released by Oxford Nanopore recently? And what are PacBio's plans for clinical sequencing? Join us in the second installment of NGS 2014.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.

Illumina Dominates NGS with Still Much Room for Improvement


Shawn Baker, Chief Scientific Officer, AllSeq

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Listen (3:39) #AGBT14: to tweet or not to tweet

Listen (6:23) Illumina solidifies dominance

Listen (6:07) The Wizard of Oxford?

Listen (4:21) Qiagen with a killer workflow

Listen (2:21) Genapsys teases

Listen (1:07) Affy founder with a new technology

Listen (2:26) Aw shucks - a new reference genome

Listen (4:49) Where to from here?

Today we begin our annual sequencing series with Shawn Baker, Chief Scientific Officer at AllSeq.

In today's interview Shawn links highlights of last week's AGBT conference with the overall trends in the sequencing space. If last year was all about "long read" technology, Shawn says this year is about Illumina's total domination.

Yet there are newcomers. Qiagen is set to introduce a sequencer designed for clinical use. After picking up bioinformatics platforms, CLC Bio and Ingenuity last year, "Qiagen will have the workflow, start-to-finish, that no one else has these days," says Shawn.

The upstart Genapsys, funded by the Russian tech investor Yuri Milner, presented at AGBT with a teaser on their new sequencer with the footprint of an iPad. And Affymetrix founder, Steve Fodor, introduced a new company with a product that will integrate with NGS.

It's one of the hottest technologies in our business, and Shawn, who maintains an up-to-date Knowledge Bank at, can talk about it like no one else. Presenting NGS 2014.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.