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Markers/Short Reads: Sep 1, 2004


Last month, NHGRI added 18 organisms to its priority list of genomes to sequence. Among the lucky critters: elephant, shrew, guinea pig, hedgehog, cat, orangutan, rabbit, snail, and lamprey. Sequencing will be conducted by Agencourt Biosciences, TIGR, and the genome centers at Baylor, the Broad Institute, and Washington University.


IBM has joined forces with the Mayo Clinic, making the clinic the first medical institution to use IBM’s Blue Gene supercomputer with specialized algorithms designed to help in molecular disease modeling. Another part of the deal includes mapping patient records to new medical information including genomics and proteomics data.


MDS Proteomics has reorganized and changed its name to Protana. The company will run on a service model, performing lead optimization, protein identification and analysis, and biomarker discovery research for customers.


Cambridge University, Affymetrix, and ParAllele BioScience have teamed up to undertake a large-scale gene association study aimed at finding genes implicated in diabetes. Researchers will use SNP panels from ParAllele to genotype some 2,000 people and analyze more than 20,000 DNA samples already collected.


This summer, NHGRI launched a Web resource designed to help people find legal and policy information related to genetic issues. The searchable database, which can be found at, focuses on genetic testing, insurance discrimination, patenting, and other subjects.


Affymetrix filed suit against Illumina on claims of patent infringement. The patents at issue — six of them — cover various aspects of arrays, hardware, and software. Illumina said it would “vigorously defend itself against these allegations.”


Teenagers might be able to feel a little less self-conscious in the coming years. Researchers recently sequenced the genome of the bacterium that causes acne, finding 2,333 genes and identifying some directly responsible for causing inflammation.


After trying its darnedest, Sequenom finally gave up on its vision of becoming a pharmaceutical firm. The company shuttered its internal drug discovery efforts and its pharmaceuticals business unit — a move that will mean annual savings of $10 million and reducing its staff by 50 people by the end of this year — opting to focus instead on its genetics systems business division. In other news, Sequenom announced a collaboration with NHGRI to perform gene expression on genes linked to diabetes susceptibility.


Celera Genomics announced plans to sell its Rockville, Md., facility. The company wrote off the $18.1 million loss it expects to incur from selling the facility, which has two buildings. Celera plans to lease the facility back from the new owners and keep its proteomics and bioinformatics divisions working there.


Mexico’s National Institute of Health announced plans to build a national medical genomics center in a nationwide effort to improve healthcare. The goal of the center will be to apply genomics knowledge to help predict and prevent health problems.


Nanosphere expanded its agreement to develop technology that would detect DNA sequences of bioweapons and could be sent into the field. The deal, originally signed in 2002, is with the US Government Technical Support Working Group. Recently, the company also received a $2.5 million grant from the same agency to continue work on its technology.


Shamrock Structures, based in Woodbridge, Ill., will provide integrated structural proteomics services to Intra-Cellular Therapies in a new deal. Shamrock will handle crystallization work, synchrotron data collection, and protein-target-related research for Intra-Cellular, which focuses on central nervous system disorders.


The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.