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1.  HLA Typing from 1000 Genomes Whole Genome and Whole Exome Illumina Data 
PLoS ONE  2013;8(11):e78410.
Specific HLA genotypes are known to be linked to either resistance or susceptibility to certain diseases or sensitivity to certain drugs. In addition, high accuracy HLA typing is crucial for organ and bone marrow transplantation. The most widespread high resolution HLA typing method used to date is Sanger sequencing based typing (SBT), and next generation sequencing (NGS) based HLA typing is just starting to be adopted as a higher throughput, lower cost alternative. By HLA typing the HapMap subset of the public 1000 Genomes paired Illumina data, we demonstrate that HLA-A, B and C typing is possible from exome sequencing samples with higher than 90% accuracy. The older 1000 Genomes whole genome sequencing read sets are less reliable and generally unsuitable for the purpose of HLA typing. We also propose using coverage % (the extent of exons covered) as a quality check (QC) measure to increase reliability.
PMCID: PMC3819389  PMID: 24223151
2.  Investigating the Effects of Simulated Martian Ultraviolet Radiation on Halococcus dombrowskii and Other Extremely Halophilic Archaebacteria 
Astrobiology  2009;9(1):104-112.
The isolation of viable extremely halophilic archaea from 250-million-year-old rock salt suggests the possibility of their long-term survival under desiccation. Since halite has been found on Mars and in meteorites, haloarchaeal survival of martian surface conditions is being explored. Halococcus dombrowskii H4 DSM 14522T was exposed to UV doses over a wavelength range of 200–400 nm to simulate martian UV flux. Cells embedded in a thin layer of laboratory-grown halite were found to accumulate preferentially within fluid inclusions. Survival was assessed by staining with the LIVE/DEAD kit dyes, determining colony-forming units, and using growth tests. Halite-embedded cells showed no loss of viability after exposure to about 21 kJ/m2, and they resumed growth in liquid medium with lag phases of 12 days or more after exposure up to 148 kJ/m2. The estimated D37 (dose of 37 % survival) for Hcc. dombrowskii was ≥ 400 kJ/m2. However, exposure of cells to UV flux while in liquid culture reduced D37 by 2 orders of magnitude (to about 1 kJ/m2); similar results were obtained with Halobacterium salinarum NRC-1 and Haloarcula japonica. The absorption of incoming light of shorter wavelength by color centers resulting from defects in the halite crystal structure likely contributed to these results. Under natural conditions, haloarchaeal cells become embedded in salt upon evaporation; therefore, dispersal of potential microscopic life within small crystals, perhaps in dust, on the surface of Mars could resist damage by UV radiation.
PMCID: PMC3182532  PMID: 19215203
Halococcus dombrowskii; Simulated martian UV radiation; LIVE/DEAD staining; Halite fluid inclusions; UV transmittance and reflectance; Desiccation

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