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TRIG Working Group Lecture References
Lecture I: Genomic Pathology: An Introduction
Authors: Richard L. Haspel, MD, PhD; Mark S. Boguski, MD, PhD
Ashley EA, et al. Clinical assessment incorporating a personal genome. Lancet. 2010;
375:1525.
Choi M, et al. Genetic diagnosis by whole exome capture and massively parallel DNA
sequencing. Proc Natl Acad Sci U S A. 2009; 106:19096.
Feero WG, Green ED. Genomics education for health care professionals in the 21st
century. JAMA. 2011; 306:989.
Jones SJ, et al. Evolution of an adenocarcinoma in response to selection by targeted
kinase inhibitors. Genome Biol. 2010; 11: R82.
Kahvejian A. et al. What would you do if you could sequence everything? Nat
Biotechnol. 2008; 26: 1125.
Link DC, et al. Identification of a novel TP53cancer susceptibility mutation through
whole-genome sequencing of a patient with therapy-related AML. JAMA. 2011; 305:
1568.
Lupski JR, et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth
neuropathy. N Engl J Med. 2010; 362:1181.
Macarthur D. Sample swaps at 23andMe: a cautionary tale. Wired. 2010;
http://www.wired.com/wiredscience/2010/06/Sample-swaps-at-23andMe:-a-cautionarytale; accessed 2/10/12.
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National Human Genome Research Institute. The human genome project completion:
Frequently asked questions. http://www.genome.gov/11006943; accessed 2/10/12.
Roychowdhoury S, et al. A model for pathology and genomics Sci Transl Med. 2011; 3:
111ra121.
Salari K. The Dawning Era of Personalized Medicine Exposes a Gap in Medical
Education. PLoS Medicine. 2009; 6: e1000138
Welch JS, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene.
JAMA, 2011; 305: 1577.
Worthey EA, et al. Making a definitive diagnosis: Successful clinical application of
whole exome sequencing in a child with intractable inflammatory bowel disease.
Genetics in Medicine 2011; 13: 255.
Lecture II: Genomic Methods
Authors: Dennis P. Wall, PhD; Frederic G. Barr, MD, PhD; Debra G.B. Leonard, MD,
PhD
Alsmadi OA, et al. High accuracy genotyping directly from genomic DNA using a rolling
circle amplification based assay. BMC Genomics. 2003 4:21.
Duggan DJ, et al. Expression profiling using cDNA microarrays. Nature Genetics 1999;
21:10.
Hung RJ, et al. A susceptibility locus for lung cancer maps to nicotinic acetylcholine
receptor subunit genes on 15q25. Nature Genetics. 2008; 452: 633.
Jones SJ, et al. Evolution of an adenocarcinoma in response to selection by targeted
kinase inhibitors. Genome Biol. 2010; 11: R82.
Koboldt DC et al. Challenges of sequencing human genomes. Brief Bioinform. 2010; 11:
484.
LaFramboise T. Single nucleotide polymorphism arrays: a decade of biological,
computational and technological advances. Nucleic Acids Res. 2009; 37: 4181.
Li H, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;
25:2078.
Miller DT, et al. Consensus statement: Chromosomal microarray is a first-tier clinical
diagnostic test for individuals with developmental disabilities or congenital anomalies.
Amer J Hum Genet. 2010; 86:749.
Ng PC, et al. An agenda for personalized medicine. Nature. 2009; 461: 724.
2
Perou CM, et al. Expression profile breast ca Molecular portraits of human breast
tumours. Nature. 2000; 406: 747.
Roychowdhoury S, et al. A model for pathology and genomics Sci Transl Med. 2011; 3:
111ra121.
Teo YY. Common statistical issues in genome-wide association studies: a review on
power, data quality control, genotype calling and population structure. Curr Op in
Lipidology. 2008; 19:133.
Welch JS, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene.
JAMA, 2011; 305: 1577.
Online Resources
• Online Mendelian Inheritance in Man (http://www.ncbi.nlm.nih.gov/omim)
• International HapMap project (http://hapmap.ncbi.nlm.nih.gov)
• Human genome mutation database (http://www.hgvs.org/dblist/glsdb.html)
• PharmGKB (http://www.pharmgkb.org)
Lecture III: Interpreting Genomic Information for Clinical Care
Authors: Richard L. Haspel, MD, PhD; Karen L. Kaul, MD, PhD; Henry M. Rinder, MD
Alpha-tocopherol, Beta-carotene Cancer Prevention Study Group. The effect of vitamin
E and beta-carotene on the incidence of lung cancer and other cancers in male smokers.
NEJM 1994; 330: 1029.
Alsmadi OA, et al. High accuracy genotyping directly from genomic DNA using rolling
circle amplification based assay. BMC Genomics. 2003 4:21.
Ashley EA, et al. Clinical assessment incorporating a personal genome. Lancet. 2010;
375:1525.
Cuzick J, et al. Prognostic value of a combined estrogen receptor, progesterone receptor,
Ki-67, and human epidermal growth factor receptor 2 immunohistochemical score and
comparison with the genomic health recurrence score in early breast cancer. J Clin Oncol.
2011; 29: 4273.
Fan HC, et al. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA
from maternal blood. PNAS. 2008; 105: 16266.
Hung RJ, et al. A susceptibility locus for lung cancer maps to nicotinic acetylcholine
receptor subunit genes on 15q25. Nature Genetics. 2008; 452: 633.
Jones SJ, et al. Evolution of an adenocarcinoma in response to selection by targeted
kinase inhibitors. Genome Biol. 2010; 11: R82.
3
Lagakos SW. The challenge of subgroup analyses — reporting without distorting.
NEJM. 2006; 354: 16.
Menkes MS, et al. Serum beta-carotene, vitamins A and E, selenium and the risk of lung
cancer. NEJM 1986; 315:1250;
Ng PC, et al. An agenda for personalized medicine. Nature. 2009; 461: 724.
Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA.
2008; 299: 1335.
Perou CM, et al. Molecular portraits of human breast tumours. Nature. 2000; 406: 747.
Srinivasan BS, et al. A universal carrier test for the long tail of Mendelian disease.
Reprod Biomed Online. 2010; 21: 537-51.
Welch JS, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene.
JAMA, 2011; 305: 1577.
Lecture IV: Genomic Medicine: Communicating with the Patient
Authors: Julianne O’Daniel, MS, CGC; Joan Scott, MS, CGC; Elizabeth Varga, MS,
CGC; VO Speights, DO; Erynn Gordon, MS, CGC
Ashley EA, et al. Clinical assessment incorporating a personal genome. Lancet. 2010;
375:1525.
Bloss CS, et al. Effect of Direct-to-Consumer Genomewide Profiling to Assess Disease
Risk. NEJM. 2011; 364: 524.
Macarthur D. Sample swaps at 23andMe: a cautionary tale. Wired. 2010;
http://www.wired.com/wiredscience/2010/06/Sample-swaps-at-23andMe:-a-cautionarytale; accessed 2/10/12.
National Society of Genetic Counselors. Professional status survey. 2010.
http://www.nsgc.org/Publications/ProfessionalStatusSurvey/tabid/142/Default.aspx;
accessed 2/10/12.
Ng PC, et al. An agenda for personalized medicine. Nature. 2009; 461: 724.
Parmigiani G, et al. Validity of models for predicting BRCA1 and BRCA2 mutations. Ann
Intern Med. 2007; 147: 441.
Robson ME, et al. American Society of Clinical Oncology Policy Statement Update:
Genetic and Genomic Testing for Cancer Susceptibility JCO. 2010; 28: 893-901.
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Roychowdhoury S, et al. A model for pathology and genomics Sci Transl Med. 2011; 3:
111ra121.
United State Preventive Services Task Force. Genetic risk assessment and BRCA
mutation testing for breast and ovarian cancer susceptibility. 2005;
http://www.uspreventiveservicestaskforce.org/uspstf/uspsbrgen.htm; accessed 2/10/12.
UT Southwestern Medical Center. Cancer Gene.
http://www8.utsouthwestern.edu/utsw/cda/dept47834/files/73815.html; accessed 2/10/12
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