Oct 16, 2012

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. 


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. 

Oct 15, 2012

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


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