Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Biomedical Sciences


Genetics, Functional Genomics, and Proteomics

Research Advisor

Robert W. Williams, Ph.D.


Hao Chen, Ph.D. Eldon E. Geisert, Ph.D. Ramin Homayouni, Ph.D. David R. Nelson, Ph.D.


BXD, complex traits, DBA/2J, nextgeneration sequencing, PheWAS, reverse genetics


Reverse genetics methods, particularly the production of gene knockouts and knockins, have revolutionized the understanding of gene function. High throughput sequencing now makes it practical to exploit reverse genetics to simultaneously study functions of thousands of normal sequence variants and spontaneous mutations that segregate in intercross and backcross progeny generated by mating completely sequenced parental lines. To evaluate this new reverse genetic method we resequenced the genome of one of the oldest inbred strains of mice—DBA/2J—the father of the large family of BXD recombinant inbred strains. We analyzed ~100X wholegenome sequence data for the DBA/2J strain, relative to C57BL/6J, the reference strain for all mouse genomics and the mother of the BXD family. We generated the most detailed picture of molecular variation between the two mouse strains to date and identified 5.4 million sequence polymorphisms, including, 4.46 million single nucleotide polymorphisms (SNPs), 0.94 million intersections/deletions (indels), and 20,000 structural variants. We systematically scanned massive databases of molecular phenotypes and ~4,000 classical phenotypes to detect linked functional consequences of sequence variants. In majority of cases we successfully recovered known genotype-to-phenotype associations and in several cases we linked sequence variants to novel phenotypes (Ahr, Fh1, Entpd2, and Col6a5). However, our most striking and consistent finding is that apparently deleterious homozygous SNPs, indels, and structural variants have undetectable or very modest additive effects on phenotypes.




Six month embargo expired June 2016

Supplementary Table 2-1.pdf (4793 kB)
Supplementary Table 2-1

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Supplementary Table 3-1.pdf (14118 kB)
Supplementary Table 3-1

Supplementary Table 3-2.pdf (446 kB)
Supplementary Table 3-2

Supplementary Table 4-1.pdf (181 kB)
Supplementary Table 4-1