Genome Sequencing in Practice: Recent Insights - July 13, 2015

Genomics|Features|Human Genome Sequencing

Human Genome Sequencing

Genome Sequencing in Practice: Recent Insights - July 13, 2015

CDC and Related Info

• Good laboratory practice for clinical next-generation sequencing informatics pipelinesGargis Amy et al. Nature Biotechnology, July 2015
• Evaluating the clinical utility of genomic variants derived from next-generation sequencing for opportunistic disease screening and risk assessment: Evidence gaps and priorities.February 5, 2015
• CDC blog post:Reconciling the future of genomic medicine with its current reality.(2014)
• CDC commentary:The arrival of genomic medicine to the clinic is only the beginning of the journey James P. Evans & Muin J. Khoury. Genetics in Medicine 15, 268-269
• Genome sequencing in the clinic – The question is not whether the glass is half-full or half-empty but whether or not the glass is the right tool.
• When should we all have our genomes sequenced?

CDC paper: Good laboratory practice for clinical next-generation sequencing informatics pipelines
Gargis Amy et al. Nature Biotechnology, July 2015

On a fast track: Can rapid genome sequencing at birth help save lives?  By Laura Beil, Genome Magazine, Jun 29

The future of next-generation sequencing in neurology.
LePichon Jean-Baptiste et al. JAMA Neurol 2015 Jul 6.

Clinical applications of next generation sequencing in cancer: from panels, to exomes, to genomes.
Shen T et al. Front Genet 2015 215

Clinical applications of next-generation sequencing in histocompatibility and transplantation.
Lan JH et al. Curr Opin Organ Transplant 2015 Jun 23.

ClinGen setting standards for when genes and their variants matter in disease
Benowitz S, National Human Genome Research Institute, May 27, 2015

Curating the way to better determinants of genetic risk 
Phimister EG.NEJM Editorial, May 27, 2015

ClinGen - the clinical genome resource
Rehm HL et al. NEJM, May 27, 2015

Project brings whole genome sequencing into the clinic, Oxford University News and Blog, May 18

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders
Taylor JC et al, Nature Genetics, May 18, 2015

The utility of next-generation sequencing in diagnosis and monitoring of acute myeloid leukemia and myelodysplastic syndromes.
Duncavage EJ et al. Int J Lab Hematol 2015 May 115-21

Next generation sequencing in endocrine practice.
Forlenza GP et al. Mol. Genet. Metab. 2015 May 3.

The clinical application of genome-wide sequencing for monogenic diseases in Canada: Position Statement of the Canadian College of Medical Geneticists.
Boycott K et al. J. Med. Genet. 2015 May 7.

The theory and practice of genome sequence assembly.
Simpson JT et al. Annu Rev Genomics Hum Genet 2015 Apr 22.

High-throughput sequencing in mutation detection: A new generation of genotoxicity tests?
Maslov AY et al. Mutat. Res. 2015 Apr 20.

Whole-genome CNV analysis: advances in computational approaches.
Pirooznia M et al. Front Genet 2015 138

Hereditary cancer risk assessment: challenges for the next-gen sequencing era.
Pinheiro H et al. Front Oncol 2015 62

Cancer whole-genome sequencing: present and future.
Nakagawa H et al. Oncogene 2015 Mar 30.

More on Next Generation Sequencing: Clinical Utility and Oversight - April 29, 2015

Op-Ed: Why whole-genome testing hurts more than it helps, G Welsh and W. Burke, LA Times, Apr 28

Khoury MJ, Cashion A, Billings PR. Evaluating the clinical utility of genomic variants derived from next-generation sequencing for opportunistic disease screening and risk assessment: Evidence gaps and priorities. Institute of Medicine Discussion Report, February 5, 2015   

Clinical utility: Informing treatment decisions by changing the paradigm, 
IOM Discussion Paper, Robert McCormack et al, January 30, 2015

FDA considering how to tailor its oversight for next generation sequencing, by Margaret A. Hamburg, FDA Voice, Jan 30

Demonstrating the clinical utility of next generation sequencing in clinical oncology,  [PDF 1.70 MB] Center for Medical Technology Policy Meeting Summary (2014)

What is the difference between clinical validity and clinical utility in genomics?  See EGAPP methods articles:

The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) initiative: methods of the EGAPP Working Group (2009)

Description and pilot results from a novel method for evaluating return of incidental findings from next-generation sequencing technologies (2013)

Doctor, have you had your DNA tested? By Robert Klitzman, M.D. , New York Times, Feb 5

Genome Sequencing in Undiagnosed Diseases: Recent Insights - April 8, 2015

Exome sequencing comes to the clinic
Ricki Lewis, JAMA April 7, 2015

A genome sequencing program for novel undiagnosed diseases
Bloss C. et al. Genetics in Medicine, March 19, 2015

Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios.
Zhu X et al. Genet. Med. 2015 Jan 15.

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data.
Wright CF et al. Lancet 2014 Dec 16.

Exome sequencing in undiagnosed inherited and sporadic ataxias.
Pyle A et al. Brain 2015 Feb (Pt 2) 276-83

Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions.
Farwell KD et al. Genet. Med. 2014 Nov 6.

Exome sequencing for gene discovery in lethal fetal disorders - harnessing the value of extreme phenotypes.
Filges I et al. Prenat. Diagn. 2014 Jul 21.

Diagnostic exome sequencing to elucidate the genetic basis of likely recessive disorders in consanguineous families.
Makrythanasis P et al. Hum. Mutat. 2014 Oct (10) 1203-10

Economics of Next Generation Sequencing - February 17, 2015

Next Generation DNA Sequencing: A review of the cost effectiveness and guidelines
Ottawa (ON):Canadian Agency for Drugs and Technologies in Health 2014 Feb 6.

The cost-effectiveness of clinical sequencing
Veenstra D et al. Institute of Medicine Discussion Paper, February 2015

The cost-effectiveness of returning incidental findings from next-generation genomic sequencing.
Bennette Caroline S et al. Genet. Med. 2014 Nov 13.

How behavioral economics can help to avoid 'The last mile problem' in whole genome sequencing.
Blumenthal-Barby Jennifer S et al. Genome Med 2015 (1) 3

Genome sequencing: a systematic review of health economic evidence.
Frank Martin et al. Health Econ Rev 2013 (1) 29

Is the "$1000 Genome" really $1000? Understanding the full benefits and costs of genomic sequencing.
Phillips Kathryn A et al. Technol Health Care 2015 Feb 6.

Comparative effectiveness of next generation genomic sequencing for disease diagnosis: design of a randomized controlled trial in patients with colorectal cancer/polyposis syndromes.
Gallego Carlos J et al. Contemp Clin Trials 2014 Sep (1) 1-8

Assuring the Validity of Next Generation Sequencing - January 20, 2015

Analytic validity of genomic testing, Discussion paper, by V. Platt et al., IOM Roundtable on Genomics Translation, Jan 15

Variant validity (selected vs. general population), Discussion paper, by Billings PR, et al. IOM Roundtable on Genomics Translation, Jan 22

The CDC Genetic Testing Reference Materials Coordination Program

The Genome in a Bottle Consortium

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the clarity challenge. 
CA Brownstein, et al. Genome Biology 2014;  15(3):R53.

The American College of Medical Genetics and Genomics  clinical laboratory standards for next-generation sequencing. 
Genetics in Medicine 2013; 15(9):733–747.

Three-year experience of a CAP/ACMG methods-based external proficiency testing program for laboratories offering DNA sequencing for rare inherited disorders.
Richards CS, et al. Genetics in Medicine, January 2014

Whole Genome/Exome Sequencing in Practice: Recent Insights - December 11, 2014

Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. 
Sarah E. Soden et al. Sci Trans Med, December 3, 2014

New study validates usefulness of genomic medicine in children with neurologic disorders. Genomic tests are uncovering elusive diagnoses, saving time and money, and changing treatment for infants and children. Eureka Alert, Dec 3

Sequencing kids' exomes: More good news, by Ricki Lewis, PLOS Blogs, Dec 11

Human Genome Sequencing: Clinical Applications - October 30, 2014

Editorial: Genome-scale sequencing in clinical care: Establishing molecular diagnoses and measuring value.
Jonathan S. Berg, JAMA, October 18, 2014

Molecular findings among patients referred for clinical whole-exome sequencing  
Yaping Yang, PhD1; et al. JAMA October 18, 2014

Clinical exome sequencing for genetic identification of rare Mendelian disorders. 
Hane Lee, et al. JAMA  October 18, 2014 

CDC blog post: Reconciling the future of genomic medicine with its current reality. (2014)

CDC Commentary: The arrival of genomic medicine to the clinic is only the beginning of the journey
James P. Evans & Muin J. Khoury. Genetics in Medicine 15, 268-269 

Human Genome Sequencing: Clinical Applications - October 22, 2014

Editorial: Genome-scale sequencing in clinical care:  Establishing molecular diagnoses and measuring value.  
 Berg, JAMA, October 18, 2014

Molecular findings among patients referred for clinical whole-exome sequencing  
 Yang, PhD1; et al. JAMA October 18, 2014

Clinical exome sequencing for genetic identification of rare Mendelian disorders. 
 Lee, et al. JAMA  October 18, 2014 

Selected articles from Nature special web collections

Next-generation sequencing in the clinic. 
Jason Y Park, Larry J Kricka & Paolo Fortina Nature Biotechnology 31, 990-992 (2013)

Genomic testing reaches into the womb. 
Malorye Allison. Nature Biotechnology 31, 595-601 (2013)

Next-generation sequencing for research and diagnostics in kidney disease
Kirsten Y. Renkema, et al. Nature Reviews Nephrology 10, 433-444 (2014)

Exploration of liver cancer genomes. 
Tatsuhiro Shibata & Hiroyuki Aburatani. Nature Reviews Gastroenterology & Hepatology 11, 340-349 (2014)

Molecular genetic testing and the future of clinical genomics
Sara Huston Katsanis & Nicholas Katsanis. Nature Reviews Genetics 14, 415-426 (2013)

The expanding scope of DNA sequencing.
Jay Shendure & Erez Lieberman Aiden Nature Biotechnology 30, 1084-1094 (2012)

Pharmacogenomics in clinical practice and drug development
Andrew R Harper & Eric J Topol. Nature Biotechnology 30, 1117-1124 (2012)

Whole-genome and whole-exome sequencing in neurological diseases
Jia-Nee Foo, Jian-Jun Liu & Eng-King Tan. Nature Reviews Neurology 8, 508-517 (2012)

Implementing personalized cancer genomics in clinical trials
Richard Simon & Sameek Roychowdhury. Nature Reviews Drug Discovery 12, 358-369 (2013)

Disease-targeted sequencing: a cornerstone in the clinic
Heidi L. Rehm. Nature Reviews Genetics 14, 295-300 (2013)

Next-generation sequencing in the clinic: are we ready?
Leslie G. Biesecker, et al. Nature Reviews Genetics 13, 818-824 (2012)

CDC blog post: Reconciling the future of genomic medicine with its current reality. (2014)

CDC Commentary: The arrival of genomic medicine to the clinic is only the beginning of the journey
James P. Evans & Muin J. Khoury. Genetics in Medicine 15, 268-269 

Whole exome sequencing closer to becoming 'new family health history', Science Cordex, Oct 18

Translating Whole Genome Sequencing: Investing in Future Healthcare - August 7, 2014

The genetic building blocks of future healthcare, Wellcome Trust, Aug 1

Human genome: UK to become world number 1 in DNA testing, UK Government, Aug 1

A new era for healthcare, by Dr Hilary Burton, PHG Foundation, Aug 1

Genomics is not overhyped: it really can change medicine, The Telegraph, Aug 1

Assessing genomic sequencing information for health care decision making, IOM workshop report, Jul 21 

Diagnostic clinical genome and exome sequencing. 
Leslie G. Biesecker, et al. N Engl J Med 2014; 370:2418-2425, June 19, 2014

NIH research highlights: Genome sequencing is moving into doctor offices; NIH gives guidance on how to best use these new technologies

Clinician's guide for genomics. 
Bridget M. Kuehn, MSJ JAMA. 2014;312(4)

Genome sequencing on the way to clinical use in treating cancer, by Kate Marusina, Genetic Engineering and Biotechnology News, Genetic Literacy Project, Aug 4

CDC blog post: Reconciling the future of genomic medicine with its current reality.