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Mathematical Analysis of Biological Datasets

SAMM-logo-1 The SAMM Group has the expertise to write custom programs that can analyze a
vast array of biological datasets.


											

Our capabilities include, but are not
limited to:

  • Biomarker Discovery
  • Genome-Wide Association Studies
  • Survival Analysis
  • Power Calculations for Study Design
  • Statistical Analysis

Contact Information: Dr. Brian T. Luke (301)846-5553


Factors that Affect Donated Tissue Quality

The GTEx program plans to collect ?non-diseased? tissues from 900 donors for further analysis
by the end of fiscal year 2015. During the pilot phase, as per the study goal, a total of 190 cases
were collected. To refine the requirements for Scale up, many of the processes utilized in the GTEx
pilot such as quality of the collected biospecimens and accuracy of collected data were evaluated
to determine their ability to scale and to collect high quality specimens and data to meet the project goals.

This work was done in collaboration with Dr. Anita H. Undale, OBBR, Leidos Biomedical Research, Inc.

Quality (RIN) vs Collection Time (PMI)Adrenal Gland (r = -0.767)

mabd01 The color is determined by BSS

Red = RPCI(-UNYTS)

Green = NDRI-LNH

Blue = NDRI-GLDP

Yellow = SCThe shape is determined by collection type

Circle = Postmortem

Square = Organ Donor (OPO)

The internal mark is determined by autolysis value

None = 0

Vertical dash = 1

Horizontal dash = 2

?+? mark = 3


Proteomic Changes Resulting from Irradiation

In collaboration with Dr. Deborah E. Citrin, Radiation Oncology Branch, CCR,
this project examined changes in the extracellular proteome using LC/MS/MS techniques.
Suction was used to extract blister fluid from individuals immediately before irradiation,
immediately after irradiation, and one year later. Differentially expressed genes were
identified using in-house software, and then processed using DAVID to elucidate common ontologies.


Results comparing immediately before and after irradiation

Term p-value Genes TotalPop HitsPop TotalFold Enrichment Bonferroni Benjamini
GO:0030529~ribonucleoprotein complex 3.36E-09 Q12906, Q12905,
P69905, ?
93 515 12782 5.337509 7.80E-07 3.90E-07
GO:0003729~mRNA binding 1.91E-06 P27797, Q08257,
P23396, ?
117 66 12983 13.5404 5.02E-04 1.67E-04
GO:0003723~RNA binding 5.08E-06 Q12906, Q12905,
P05387, ?
117 718 12983 3.245518 1.336E-03 3.34E-04
RNA binding 3.92E-05 Q12906, P06748,
P23588, ?
123 540 19235 4.054351 9.753E-03 7.54E-04
ribonucleoprotein 4.10E-04 P62314, P05387,
P39019, ?
123 279 19235 5.044584 0.0974 0.004446