All students were required to respond to each paper (PDF).
|1||Human Variation: Challenges in human genomics, Variation, haplotypes, LD, Common and rare variant association||
Lander. “Initial Impact of the Sequencing of the Human Genome.” Nature 470 (2011): 187–97.
The 1000 Genomes Project Consortium. “A Global Reference for Human Genetic Variation.” Nature 526, no. 7571 (2015): 68–74.
|2||Trait Association: Common and rare variant association, Mendelian vs. Complex, Basics of an association study, Phenotypes||
Lander, Eric S., and Nicholas J. Schork. “Genetic Dissection of Complex Traits.” Science 265, no. 5181 (1994): 2037–48.
Altshuler, et al. “Genetic Mapping in Human Disease.” Science 322, no. 5903 (2008): 881–8.
Zuketal. “Searching for Missing Heritability: Designing Rare Variant Association Studies.” Proceedings of the National Academy of Sciences of the United States of America 111, no. 4 (2014): E455–64.
|3||Personal Genomics and Ethics: Research studies: Consent, privacy, returning results, Medical applications: Testing, public health issues, obligations to relatives, privacy, Consumer options: Carrier testing, newborn testing, genetic testing, Gene editing: Beneﬁts, ethical issues, where to draw the line||
Hudson. “Genomics, Health Care, and Society.” The New England Journal of Medicine, no. 365 (2011): 1033–41.
Fulda, and Lykens. “Ethical Issues in Predictive Genetic Testing: A Public Health Perspective.” Journal of Medical Ethics 32, no. 3 (2006): 143–7.
Prenatal / Newborns
Lanphier, et al. “Don’t Edit the Human Germ Line.” Nature 519, no. 7544 (2015).
|4||Interpreting Coding (Rare) Variants: Rare variant detection from exome sequencing in family studies, Aggregate analyses (e.g. ExAC), Classifying function (PolyPhen), Overlapping constraint||
Adzhubei, et al. “A Method and Server for Predicting Damaging Missense Mutations.” Nature Methods 7, no. 4 (2010): 248–9.
Exome Aggregation Consortium. “Analysis of Protein-coding Genetic Variation in 60,706 Humans.” Nature 536, no. 7616 (2015): 285–91.
Homsy, et al. “De Novo Mutations in Congenital Heart Disease with Neurodevelopmental and Other Congenital Anomalies.” Science 350, no. 6265 (2015): 1262–6.
Flannick, et al. “Loss-of-function Mutations in SLC30A8 Protect Against Type 2 Diabetes.” Nature Genetics 46, no. 4 (2014): 357–63.
|5||Interpreting Non-Coding (Common) Variants: Enriched cell types, Causal variants: Epigenomics, Comparative Genomics, Target genes: HiC, genetic links, activity links, Upstream regulators: Regulatory motifs, TF binding||
Ward, and Kellis. “Interpreting Noncoding Genetic Variation in Complex Traits and Human Disease.” Nature Biotechnology 30 (2012): 1095–106.
Kundaje, et al. “Integrative Analysis of 111 Reference Human Epigenomes.” Nature 518, no. 7539 (2015): 317–30.
Claussnitzer, et al. “FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.” The New England Journal of Medicine 373 (2015): 895–907.
|6||Bayesian Fine-Mapping and Multi-dimensional GWAS: Fine-mapping (Posterior probabilities). Bayesian models for computational ﬁne-mapping, Multi-dimensional GWAS (Multi-Phenotype, Multi-ancestry, Multi-variant)||
Pickrell. “Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits.” Cell 94, no. 4 (2014): 559–73.
Kichaev, et al. “Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies.” PLOS Genetics (2014).
|7||Intermediate Phenotypes and QTLs: eQTLs, meQTLs, and other molecular traits, Allelic activity, Causality and mediation analysis, Mendelian randomization analysis||
The GTEx Consortium. “The Genotype-Tissue Expression (GTEx) Pilot Analysis: Multitissue Gene Regulation in Humans.” Science 348, no. 6235 (2015): 648–60.
Baran, et al. “The Landscape of Genomic Imprinting Across Diverse Adult Human Tissues.” Genome Resource 25 (2015): 927–36.
Liu, Aryee, et al. “Epigenome-wide Association Data Implicate DNA Methylation as an Intermediary of Genetic Risk in Rheumatoid Arthritis.” Nature Biotechnology 31 (2013): 142–7.
|8||Heritability and Phenotype Prediction: Missing heritability, heritability estimation, heritability partitioning, Polygenic risk scores, Predicting intermediate phenotypes||
Golan, et al. “Measuring Missing Heritability: Inferring the Contribution of Common Variants.” Proceedings of the National Academy of Sciences of the United States of America 111, no. 49 (2014): 5272–81.
Gusev, et al. “Partitioning Heritability of Regulatory and Cell-type-specific Variants Across 11 Common Diseases.” The American Journal of Human Genetics 95, no. 5 (2014): 535–52.
Gamazon, et al. “A Gene-based Association Method for Mapping Traits Using Reference Transcriptome Data.” Nature Genetics 47 (2015): 1091–8.
|9||Human Ancestry and Population Genetics: Coalescent theory. Recent Selection, Sweeps, Selection Pressures, Population Stratiﬁcation. Admixture Mapping, Ancestral genome sequencing and analysis||
Novembre, et al. “Genes Mirror Geography Within Europe.” Nature 456 (2008): 98–101.
Sabeti, et al. “Positive Natural Selection in the Human Lineage.” Science 312, no. 5780 (2006): 1614–20.
Sankararaman, et al. “The Genomic Landscape of Neanderthal Ancestry in Present-day Humans.” Nature 507, no. 7492 (2014): 354–7.
|10||Cancer Genomics and Single-Cell Genomics: Genetic alterations: Somatic mutations, mutational signatures, rearrangements, Epigenetic alterations: Methylation, miRNAs, reprogramming, origin, Convergence at the regulatory region, gene, pathway, cellular level. Guiding convergence with physical, genetic, and activity networks||
Cancer Genome Atlas. “Comprehensive Molecular Portraits of Human Breast Tumours.” Nature 490, no. 7418 (2012): 61–70.
Lawrence, et al. “Mutational Heterogeneity in Cancer and the Search for New Cancer-associated Genes.” Nature 499, no. 7457 (2013): 214–8.
Patel, et al. “Single-cell RNA-seq Highlights Intratumoral Heterogeneity in Primary Glioblastoma.” Science 344, no. 6190 (2014): 1396–401.
|11||Experimental Manipulations: Genome editing and CRISPR, Experiment multiplexing, Screening and selection||
Gaj, et al. “ZFN, TALEN, and CRISPR / Cas-based Methods for Genome Engineering.” Trends Biotechnology 31, no. 7 (2013): 397–405.
Melnikov, et al. “Systematic Dissection and Optimization of Inducible Enhancers in Human Cells Using a Massively Parallel Reporter Assay.” Nature Biotechnology 30, no. 3 (2012): 271–7.
Koike-Yusa, et al. “Genome-wide Reces-sive Genetic Screening in Mammalian Cells With a Lentiviral CRISPR-guide RNA Library.” Nature Biotechnology 32, no. 3 (2014): 267–73.