Mutation linked to relapse in childhood ALL

Julia Meyer is a Ph.D. student in the lab of Bill Carroll in the NYU Cancer Institute, and I have the good luck to sit on her thesis advisory committee. Julia has been using RNA-seq to look for mutations that are specific to relapse of childhood acute lymphoblastic leukemia (ALL). ALL can often be cured in children, but years after remission about 20% of patients relapse, and prognosis for relapsed ALL is very poor. 

Julia studied pairs of RNA samples from 10 patients taken at original diagnosis and again after relapse (Illumina RNA-seq). The data analysis was very difficult since she initially found millions of variants, and even after extensive stringent filtering and matching between diagnosis and relapse, there were many false positives. Eventually she narrowed it down to just 20 non-synonymous mutations that were specific to the relapse samples. Two patients harbored (different) relapse-specific mutations in the same gene, NT5C2, which codes for the Cytosolic 5’-nucleotidase II. Full exon sequencing of NT5C2 was completed in 61 additional relapse specimens (using 454 amplicon protocol), identifying 5 additional mutations which were also confirmed as relapse specific. 

Conclusions: Mutations in NT5C2 are associated with the outgrowth of drug resistant cells in childhood ALL.

This work was published as an ASCO abstract at the 2012 ASCO annual meeting. 

http://www.asco.org/ASCOv2/Meetings/Abstracts?&vmview=abst_detail_view&confID=114&abstractID=94400

As a member of the thesis committee, I got a view of some really interesting followup studies. The NT5C2 gene product is a purine nucleotidase. Structural modeling of the relapse-associated mutations in the encoded protein  suggests alteration of enzyme subunit association/dissociation. Julia has found that cells transfected with the mutant version of the NT5C2 are RESISTANT to 6-mercaptopurine, which is one of the drugs used for long term maintenance chemotherapy of ALL. She also found very low levels of the mutant allele in some diagnosis samples (early stage disease). The obvious implication is that under long term drug treatment, a clone of tumor cells with activating mutations in NT5C2 increases and create a drug resistant relapse. 

Wow. This is the first molecular model for the cause of relapse of ALL. It could lead directly to diagnostics and therapy. 

My Next-Generation DNA Sequencing Informatics book has gone live on the Cold Spring Harbor Laboratory Press website (pre-orders).

http://www.cshlpress.com/link/nextgendna.htm

It has the following chapters (see below). I am going to leak a few pages as a teaser, so I need to know which chapter is most interesting to some random selection of people. Votes will be counted in the comment section for this post.

1. Introduction to DNA Sequencing

Stuart Brown

2. History of Sequencing Informatics

Stuart Brown

3. Visualization of Next-Generation Sequencing Data

Phillip Ross Smith, Kranti Konganti, and Stuart Brown

4. DNA Sequence Alignment

Efstratios Efstathiadis

5. Genome Assembly Using Generalized de Bruijn Digraphs

D. Frank Hsu

6. De Novo Assembly of Bacterial Genomes from Short Sequence Reads

Silvia Argimón and Stuart Brown

7. Genome Annotation

Steven Shen

8. Using NGS to Detect Sequence Variants

Jinhua Wang, Zuojian Tang, and Stuart Brown

9. ChIP-seq

Zuojian Tang, Christina Schweikert, D. Frank Hsu, and Stuart Brown

10. RNA Sequencing with NGS

Stuart Brown, Jeremy Goecks, and James Taylor

11. Metagenomics

Alexander Alekseyenko and Stuart Brown

12 High-Performance Computing in DNA Sequencing Informatics

Efstratios Efstathiadis

New Blog on Next Generation Sequencing

I have started writing a new blog "channel" about Next Generation Sequencing for a website called BiteSizeBio. The first article went live today:

NGS- A Revolution in Technology

These articles will be more basic and broad then the internal lab stuff (and random personal observations) that I post here. I plan to write about one per month, and I will probably post links here when they go live.

I gave a short presentation at the NYU CTSI Translational Research in Progress seminar this week about our sequencing work on strains of Streptococcus mutans associated with severe tooth decay in children.  We sequenced and did de novo assembly on each of 20 strains, then did an in silico subtraction to find unique genomic elements associated with health or disease.

the details are in this PDF file:

https://www.box.com/s/fbea9b1d5cdb96f07348

I led a workshop on 7/31/2012 about NGS for Drug Development at this Hanson Wade conference in Boston:

NGS Bioinformatics for Drug Developers

I made a huge PPT slide deck to fill 2 hours, but in the workshop we ended up in a multi-way discussion for most of the time, so I never got to show half the slides.  I am posting them on BOX.com
so I don't feel like the effort was wasted.

NGS drug dev PPT slides