Rushed Review by Nature Biotechnology on a Cancer Bioinformatics Paper?

One of our readers, who is a PhD student, has been struggling with trying to figure out what is going on with the paper - “Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes”. The corresponding author is broadster Gad Getz, who did not respond to his email correspondences.

In addition to his role at the Broad, Getz is a co-principal investigator in the Genome Data Analysis Center (GDAC) of the NCI/NHGRI TCGA (The Cancer Genome Atlas) project; a co-leader of the International Cancer Genome Consortium (ICGC) Pan-Cancer Analysis of Whole Genomes (PCAWG) project; a co- principal investigator of the Broad-led NCI Cloud Pilot; and a member of various NCI advisory committees. In addition, Getz directs the Bioinformatics Program at the Massachusetts General Hospital Cancer Center and Department of Pathology and serves as an associate professor of pathology at Harvard Medical School. Getz is also the inaugural incumbent of the Paul C. Zamecnik Chair in Oncology at the MGH Cancer Center. He has published numerous papers in recent years in prominent journals that describe new genes and pathways involved in different tumor types.

Maybe it is time for him to publish in real scientific journals instead than ‘prominent’ magazines.

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Here are the specific questions -

The article compares a number of algorithms, but provides no details about any of the software versions or parameter settings. It’s in contrast to the editorial position presented in

http://www.nature.com/nbt/journal/v33/n4/full/nbt.3202.html which states “Since last October, all Nature journals have required that authors declare the location and accessibility of any custom code and software central to the main claims in a paper …” If the method has double the accuracy of some existing methods, I’d like to see what parameters they used on the existing methods or what versions they ran. Remarkably, the authors didn’t even provide any of the parameters of their own software, making none of their analyses reproducible. With poor quality documentation like shown below, it would be necessary to have reproducible code.

Input parameters:

-bam: path to the BAM file to be used for HLA typing

… …

-format: fastq format (STDFQ, ILMFQ, ILM1.8 or SLXFQ; see Novoalign documentation)

Source : https://www.broadinstitute.org/cancer/cga/polysolver_run

Why is the input a BAM file, but there’s a parameter to specify the FASTQ format ? Which parameters are optional and which are mandatory ? The documentation must have been an afterthought.

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I’ve also noticed they have a crucial supplementary table 11 missing from their supplementary materials and described as being available in dbGaP, but is nowhere to be found.