Contact:
mlinderman@middlebury.edu
Office:
McCardell Bicentennial Hall 633
Department of Computer Science
Middlebury College
Middlebury, VT 05753
Office Hours (Fall 2018):
M: 12:00 - 2:00 PM
T: 2:30 - 4:00 PM
W: 10:00 AM - 12:00 PM
Or by appointment

PAPG Longitudinal Impacts Paper Published

The PAPG team reported the impacts of incorporating personal whole genome sequencing into “Practical Analysis of Your Personal Genome” (PAPG), a novel laboratory-style medical genomics in which students have the opportunity to sequence their own genome. The paper, “Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years” in BMC Medical Genomics, describes student attitudes towards genome sequencing, decision-making, psychological wellbeing, genomics knowledge and pedagogical engagement across the 2013-2015 iterations of the course (a total of 59 students). This paper expands upon previous reports on the initial 19 PAPG students.

DECA (Distributed Exome CNV Analyzer) 0.20 Released

DECA (Distributed Exome CNV Analyzer) 0.20 was released today as part of the ADAM 0.23 release. DECA is a distributed implementation of the XHMM CNV calling algorithm using ADAM and Apache Spark that achieves an order of magnitude speedup on multicore workstations and Hadoop clusters. Starting from the target read depths, DECA can call CNVS in all 2535 1000 Genomes Phase 3 exomes samples in 31 minutes or less. Starting from the aligned BAM files, DECA can call CNVS in the Phase 3 exome cohort in less than 5 hours on a 56-node Hadoop cluster. Interested users are pointed to the DECA documentation and the Hacker News discussion.

PAPG in the AAMCNews

Our Practical Analysis of Your Personal Genome (PAPG) laboratory-style genomics course was recently described in an article in AAMCNews “Medical Students Learn From Analyzing Their Own Genetic Makeup”.

HealthSeq Outcomes Paper Published

The HealthSeq team reported the initial outcomes data from their longitudinal study of ostensibly healthy adults who underwent whole genome sequencing (WGS). The paper, “Psychological and Behavioural Impact of Returning Personal Results from Whole-GenomeSsequencing: The HealthSeq Project.” in the European Journal of Human Genetics, described outcomes one week and 6 months after participants received their genomic results. This paper complements earlier publications on participant’s motivations, concerns and preferences and the impact of genomic counseling on informed decision-making by HealthSeq participants.