Dec 18, 2018
Dec 18, 2018
100K Genomes Project
100K Genomes Project
Integration and interpretation of genomic information for the clinical care of solid neoplasms Salvador J. Diaz-Cano 100,000 Genomes Project – NHS England and Genomics England Royal College of Pathologists. December 18, 2018
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Coming to a clinic near you… PRELIMINARY COMMUNICATION
Open Access
StevenPRELIMINARY JM Jones1*, Janessa Laskin2, Yvonne Y Li1, Obi L Griffith1, Jianghong An1, Mikhail Bilenky1, Yaron S Butterfield1, Timothee Cezard1, Eric Chuah1, Richard Corbett1, Anthony P Fejes1, Malachi Griffith1, COMMUNICATION John Yee3, Montgomery Martin2, Michael Mayo1, Nataliya Melnyk4, Ryan D Morin1, Trevor J Pugh1, Tesa Severson1, Sohrab P Shah4,5, Margaret Sutcliffe2, Angela Tam1, Jefferson Terry4, Nina Thiessen1, Thomas Thomson2, Richard Varhol1, Thomas Zeng1, Yongjun Zhao1, Richard A Moore1, David G Huntsman3, Inanc Birol1, Martin Hirst1, Robert A Holt1, Marco A Marra1 Abstract
Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene
Background: Adenocarcinomas of the tongue are rare and represent the minority (20 to 25%) of salivary gland tumors affecting the tongue. We investigated the utility of massively parallel sequencing to characterize an adenocarcinoma of the tongue, before and after treatment.
Results: In the pre-treatment tumor we identified 7,629 genes within regions of copy number gain. There were John Welch, MD, PhD increased expression 1,078S.genes that exhibited to the blood and unrelated and four genes Context relative Whole-genome sequencing is becomingtumors increasingly available for research purposes, it has not yet beenthe routinely clinical diagnosis. Peter Westervelt, MD, PhD contained somatic protein-coding mutations. Ourbut analysis suggested tumorused cellsforwere driven by the RET oncogene. Genes whose protein products are targeted by the RET inhibitors sunitinib and sorafenib correlated with Objective To determine whether whole-genome sequencing can identify cryptic, Li Ding, PhD actionable mutations in aobservations, clinically relevant time frame. of sunitinib was beingE.amplified and or highly expressed. Consistent with our administration David Larson, PhD associated with stable disease lasting 4 Design, months,Setting, after which lung lesions toagrow. Administration and the Patient We werebegan referred difficult diagnostic caseof of acute Jeffery M. Klco, MD, PhD with no pathogenic fusion the identified by progressed routine metasorafenib and sulindac provided diseasepromyelocytic stabilization leukemia for an additional 3 monthsX-RARA after which cancer Shashikant Kulkarni, PhD A recurring phase cytogenetics or interphase fluorescence in situ hybridization (FISH). The case and new lesions appeared. metastasis possessed 7,288 genes within copy number amplicons, patient was enrolled in an institutional review board–approved protocol, with consent John Wallis,exhibiting PhD 385 genes increased expression relative to other tumors and 9 new somatic protein coding mutations. specifically tailored to the implications of whole-genome sequencing. The protocol uses Ken PhDmutations and amplifications The Chen, observed were consistent with therapeutic through a “movable firewall” that maintains patientresistance anonymityarising within the entire activation research team of the MAPK and AKTMD, pathways. but allows the research team to communicate medically relevant information to the Jacqueline E. Payton, PhD treating physician. Conclusions: WeMS conclude that complete genomic characterization of a rare tumor has the potential to aid in Robert S. Fulton, Main Outcome Measures Clinical relevance oftreatment whole-genome sequencing clinical decision making and identifying therapeutic approaches where no established protocols exist. and Joelle Veizer, BS to communicate validated resultsevolution to the treating physician. These results also provide direct in vivo time genomic evidence for mutational within a tumor under drug Heather Schmidt, BS Massively parallel paired-end sequencing allowed identification of a cytoselection and potential mechanisms of Results drug resistance accrual. Tammi L. Vickery, BS genetically cryptic event: a 77-kilobase segment from chromosome 15 was inserted en bloc into the second intron of the RARA gene on chromosome 17, resulting in a Sharon Heath classic bcr3 PML-RARA fusion gene. Reverse transcription polymerase chain reaction mutational status of protein kinases in many cancer Background Mark A. Watson, MD, PhD sequencing subsequently validated the expression of the fusion transcript. Novel FISH Large-scale sequence analysis of cancer probes transcriptomes, samplescases [4], of 623 ‘cancer genes’ in lung adenocarcinomas identified 2 additional t(15;17)–negative acute promyelocytic leukeMichael H. Tomasson, MD predominantly using expressed sequencemia tags (ESTs) [1] [5], 601 genesinsertions. in glioblastomas, and allsequencing annotatedand coding that had cytogenetically invisible Whole-genome valiDaniel C. Link, MD dation were in 7 weeks in andbreast, changedcolorectal the treatment planand for the patient. or serial analysis of gene expression (SAGE) [2,3],completed has sequences [6,7] pancreatic Timothy been usedA.toGraubert, identify MD genetic lesions that accrue during tumors sequencing [8], searching for somatic mutations that oncodrive Conclusion Whole-genome can identify cytogenetically invisible geneslarge-scale in a clinically relevant time frame. John F. DiPersio, MD,studies PhD have involved oncogenesis. Other oncogenesis. JAMA. 2011;305(15):1577-1584 www.jama.com PCR DNA The development of massively parallel sequencing Elaineamplification R. Mardis, PhDof exons and subsequent technologies has provided an unprecedented opportunity sequence analysis of the amplicons to survey the Timothy J. Ley, MD patients receiving chemotherapy variants exist but aretonot detected rapidly and by efficiently sequence human genomes [9]. Richard K. Wilson, PhD 13 alone). standard reverse transcription poly- has Such technology been applied to the identification 5-7 * Correspondence:
[email protected] merase chain reactionof(RT-PCR) ; alCUTE PROMYELOCYTIC 1 genome rearrangements in lung cancer cell lines [10], Genome Sciences Centre, British ColumbiaLEUKE Cancer- Agency, 570 West 7th HISTORY ex- CASE mia BC, (APL) commonly ternative X-RARA fusions Avenue, Vancouver, V5Z 4S6,isCanada and also the may sequencing of a complete acute myeloid A 39-year-old woman with acute myFull list of author information is available at the end ofist theand articlemay be responsive to all-trans (!90%) associated with PML-RARA (NCBI Entrez retinoic acid (ATRA) (eg, NuMA1- eloid leukemia (AML) in first remis© 2010 Jones et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons RARA, NPM1-RARA, STAT5B-RARA, Gene 5371 and 5914) fusion tran-License Attribution (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andofreproduction in Author Affiliations: Departments Medicine (Drs PRKAR1A-RARA, FIP1L1-RARA, any medium, the original work is properly cited. scripts resulting from pathogenic t(15; provided Welch, Westervelt, Tomasson, Link, Graubert, DiPer17) translocations.1,2 Unusual cytoge- BCOR-RARA, and the non-RARA trans- sio, and Ley and Ms Heath), Pathology and Immu1,8-12 or ATRA re- nology (Drs Klco, Kulkarni, Payton, and Watson), Genetic rearrangements (eg, insertions and location NUP98-RARG) netics (Drs Kulkarni, Mardis, Ley, and Wilson), and 1 3, 4, or even 8-way translocations)2-4 can sistant (PLZF-RARA). Timely and ac- Pediatrics (Dr Kulkarni), and Genome Institute (Drs Ding, Larson, Wallis, Chen, Watson, Mardis, Ley, and also lead to PML-RARA formation. Al- curate diagnosis of APL is essential, Wilson and Mr Fulton and Mss Veizer, Schmidt, and ternative PML-RARA fusions and splice because the addition of ATRA to che- Vickery), Washington University, St Louis, Missouri. motherapy leads to substantially im- Corresponding Author: Richard K. Wilson, PhD, Genome Institute, Washington University School of Mediproved outcomes (5-year event-free sur- cine, 4444 Forest Park Blvd, PO Box 8501, St Louis, See also pp 1568 and 1596. vival of 69%, compared with 29% in MO 63108 (
[email protected]).
A
©2011 American Medical Association. All rights reserved.
JAMA, April 20, 2011—Vol 305, No. 15 1577
Identification of a Novel TP53 Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML
Daniel C. Link, MD Context The identification of patients with inherited cancer susceptibility synLaura G. Schuettpelz, MD, PhD dromes facilitates early diagnosis, prevention, and treatment. However, in many cases of suspected cancer susceptibility, the family history is unclear and genetic testing of Dong Shen, MD, PhD common cancer susceptibility genes is unrevealing. Jinling Wang, MD Objective To apply whole-genome sequencing to a patient without any significant famMatthew J. Walter, MD ily history of cancer but with suspected increased cancer susceptibility because of multiple Shashikant Kulkarni, PhD primary tumors to identify rare or novel germline variants in cancer susceptibility genes. Jacqueline E. Payton, MD, PhD Design, Setting, and Participant Skin (normal) and bone marrow (leukemia) DNA Jennifer Ivanovich,a MS were early-onset breastZumbo and ovarian cancer (negative for BRCA1 b, Paul b, Ahmet c, Murim Choi , Ute I. Scholla, Weizhen Jiaobtained , Tiewenfrom Liuaa, patient Irina R.with Tikhonova Nayir Paul J. Goodfellow, PhD andSanjad BRCA2e,mutations) and therapy-related acute myeloid leukemia (t-AML) and analyzed d, Sami a, Anita a, Shrikant b, ¨ Ays! in Bakkalog˘lud, Seza Ozen Carol Nelson-Williams Farhi Mane with the following: whole-genome sequencing using paired-end reads, single-nucleotide Michelle LeRichard Beau, PhD and P. Liftona,1 polymorphism (SNP) genotyping, RNA expression profiling, and spectral karyotyping. Daniel aC. Koboldt, MS Department of Genetics, Howard Hughes Medical Institute, bKeck Foundation for Biotechnology Resources, Yale University School of Medicine, New B RIEF R EPORT Main Outcome Measures Structural variants, copy number alterations, singlecDepartment of Pediatric Nephrology, Istanbul Medical Faculty, Istanbul 34390, Turkey; dDepartment of Pediatric Nephrology David J.Haven, Dooling, PhD and CT 06510; eAmerican University of Beirut, Beirut 11072020, Lebanon Rheumatology, Hacettepe University Faculty nucleotide of Medicine, Ankara 06100, variants, andTurkey; small and insertions and deletions (indels) were detected and valiRobert S. Fulton, MS dated using the described platforms. Contributed by Richard R. Hugh F. Bender, MS P. Lifton, September 17, 2009 (sent for review September 8, 2009) Results Whole-genome sequencing revealed a novel, heterozygous 3-kilobase deletion coding MS genes constitute only approximately 1% of the human this DNA, is a which potentially efficient strategy LucindaProtein L. Fulton, removing exons 7-9 of TP53 inthe the human patient’sgenome, normal skin was homozygous in for genome but harbor 85% of the mutations with large effects on identification of rare functional mutations, the more so given that Kimberly D. Delehaunty, BA the leukemia DNA as a result of uniparental disomy. In addition, a total of 28 validated sodisease-related traits. Therefore, efficient strategies for selectively our current ability to interpret the functional consequences of single-nucleotide variations or indels in coding genes, 8 somatic structural variants, Catrinasequencing C. Fronick, BS coding regions (i.e.,matic complete ‘‘whole exome’’) have the sequence variation outside coding regions is highly limited. The and 12ofsomatic copy number alterations were detected in been the patient’s leukemia genome. potential to contribute rare and common utility of this approach has demonstrated in cancer, in which Elizabeth L. Appelbaum, BAto the understanding human diseases. Here we report a method for whole-exome sequencPCR amplification of individual exons has variants led to identification of Conclusion Whole-genome sequencing can identify novel, cryptic in canHeatheringSchmidt, BS coupling Roche/NimbleGen whole exome arrays to thegenes Illumina new somatic mutations with large effect (9);onnonetheless, cer susceptibility in addition to providing unbiased information the spec- PCR Rachel DNA Abbott, BS sequencing platform. We demonstrate ability to capture amplification each coding sequence trum the of mutations in a cancer genome. Elizabeth A. Worthey, PhD1,2, Alan N. Mayer, MD, PhD2,3 , Grant D.of Syverson, MD2, is cumbersome. Methods of approximately sequences2 with high enriching targeted genomic segments by2hybridization have been Michelle O’Laughlin,95% BS 1 of the targeted coding 1 JAMA. 2011;305(15):1568-1576 www.jama.com Danielsensitivity Helbling, , Benedetta B. of Bonacci, MSc Brennan Decker, , Jaime M.have Serpe, BSc , extended used for BSc 302 years (10), and recently been to the whole andBSc specificity for detection homozygous and, heterozy2 1 4 Ken Chen, PhD Trivikram Dasu, PhD Michael Tschannen, BSc by , Regan MSc Monica J. Basehore, PhD , limited by the large exome scale, (11), although their utility has been gous variants. We,illustrate theR. utility of this approach making L. an Veith, 1,2,3 1,2,3 3,5 Michael D. McLellan, BSMD, amounts of -genomic DNA by coupling tohas sequence unanticipated genetic diagnosis congenital chloride diarrhea in PhD a ANCER SUSCEPTIBILITY OF netic basisrequired for cancer Ulrich Broeckel, PhDof , Aoy Tomita-Mitchell, , IS Marjorie J. Arca, MD , andsusceptibility 2,3 syndrome, a 1,2 platforms of, modest throughput. Key PhD considerations in this referred with a suspected diagnosis ofMD Bartter ten suspected in individuals important clinical implications for theprocess Nobish Varghese, MS2,3 James T.patient Casper, MD , David A. Margolis, , David P. Bick, MD1,2,3 Martin J. Hessner, , completeness of the information renal salt-wasting disease. The diagnosis was based on the2,3 will be cost effectiveness and presenting with cancers at an prevention and John M. Routes, MD2,3, molecular James W. Verbsky, MD, PhD , obtained. Howard J. Jacob, PhD1,2,3,6 ,early detection of asRakeshfinding Nagarajan, MD, PhD of a homozygous missense D652N mutation at a position in 1,2,3 early age,iswith pri- thesociated However, genetic and David P. locus) Dimmock, MDmultiple SharonSLC26A3 Heath, (the CCRP We report adoption neoplasms. of whole-exome capture on single arrays known congenital chloride diarrhea that virmaryand cancers, or with a suggestive testing is expensive, many cases, on the famRoche/NimbleGen platform toand theinIllumina sequencing tually completely MD conserved in orthologues paralogues from Timothy A. Graubert, platform. We illustrate the utility of this approach by identification invertebrates to humans, and clinical follow-up confirmed the diagily history. The identification of the gemutations in cancer susceptibility genes apoptosis deficiency. !42mutation days posttransplant, the that child led was to ableantounexpected clinical Li Ding, PhDToaour of aAt rare in a patient Purpose: Wenosis. report male child who presented at 15 (or months with sequencing knowledge, whole-exome genome) has eat and drink, and there has been no recurrence of gastrointestinal diagnosis. perianal abscesses and proctitis, to transmural pancolitis Timothy Ley, MDbeenprogressing notJ.previously used to make a genetic diagnosis. Five additionalof Medicine Author Affiliations: Departments (Drs Link, Department of Surgery (Ms Ivanovich and Dr Gooddisease, suggesting this drove Washington the gastrointestinal disease. Walter,illness. Graubert, and Ley; Bender; and Msmutation Heath) also fellow), University, St Louis, Missouri; withGerard colocutaneous fistulae, consistent with aBartter Crohn disease-like patients suspected to have syndrome but who did not Mr have P. Zambetti, PhD report describes the identification of a novel of cause of inflammatory andunderlying Pathology and This Immunology (DrsResults Kulkarni, PayDepartment Biochemistry, St Jude Children’s The age andmutations severity of presentation suggested an in the known genes for this disease had homozygous deleteton, and Nagarajan bowel and Mrdisease. Varghese), Siteman CanResearch Hospital, Memphis, Tennessee (Drs Wang Equally importantly, it demonstrates the power of exome Richard K. Wilson, PhD Coupling of NimbleGen Whole-Exome Capture to Illumina Sequencing. immune defect; however, despite comprehensive clinical evaluation, we rious mutations in SLC26A3. These results demonstrate theofclinical cer Center; Department Pediatrics (Drs Schuettpelz and Zambetti); University patient of Chicago sequencing to render a molecular diagnosis in an individual in ComprehenThe whole-exome array capture were were unableR. to Mardis, arrive at PhD a definitivesequencing diagnosis, and thereby utility of whole-exome have implications for disease Elaine andrestricting Kulkarni); Department of Genetics, TheRoche/NimbleGen Genome sive Cancer Center, Chicago, Illinois (Dr Leprotocols Beau).
Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease
100K Genomes Project
RESEARCH
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors
Dec 18, 2018
Jones et al. Genome Biology 2010, 11:R82 http://genomebiology.com/2010/11/8/R82
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the setting of a developed novelDing, disease, all sequencing standard Author: diagnoses were exforafter DNA on the 454K.platform (11);The because clinical management. Methods: sought to identify Center the causative gene discovery andWe clinical diagnosis. (Drs Shen, Kulkarni, Dooling, Chen, Ley, Corresponding Richard Wilson, PhD, hausted, andKolbodt, illustrates howofthissequencing technology can used in a clinical Wilson, addiand Mardis; Messrs Genome Center, University of the McLellan, cost on be theWashington Illumina platformSchool is potentially mutation(s) through exome sequencing to provide the necessary setting. Genet Med 2011:13(3):255–262. and !Fulton; Fulton, Delehaunty, Fronick, lower, Medicine, 4444 Forest Park Blvd, Box 8501, Louis, considerably we adapted hybrid capture usingStthe Nimbletional information for! congenital clinical Results: Afterand Mss Bartter syndrome chloride diarrhea See also pp required 1577 and 1596.management. Appelbaum, Schmidt, Abbott, and O’Laughlin); and MO 63108 (
[email protected]). Gen personalized, 2.1M Human Exome Arrayimmunodeficiency to the Illumina DNA sequencing sequencing, we identified 16,124 variants. Subsequent analysis identinext-generation sequencing ! whole-exome sequencing ! personalKey genomes Words: genomic, medicine, clinical, platform (see Methods). These arrays tile oligonucleotides from fied a novel, hemizygous missense mutation in the X-linked inhibitor of 1568 JAMA, April 20, 2011—Vol 305, No. 15 ©2011 American Medical Association. All rights reserved. approximately 180,000 exons of 18,673 protein-coding genes and apoptosis gene, substituting a tyrosine for aa major highly role conserved andMendelian and enetic variation plays in both 551 micro-RNAs and comprise have 34.0 reported Mb of genomic sequence. functionally important cysteine. X-linked inhibitorAmong of apoptosis not ver the last year, a number of publications non-Mendelian diseases. the was approximately 2,600 1– 6an automated pipewere processed using previously associated with Crohn disease but has a central role in the the use ofResulting exome orsequence genomedata sequencing in patients. Mendelian diseases that have been solved, the overwhelming line: quality sequence reads or were aligned to the reference proinflammatory response and bacterial sensing through the NOD sigMost of these studies madefiltered use of disease cohorts families majority are caused by rare mutations that affect the function of human genome (hg18) using Maq software (12). Single nucleotide naling pathway. The mutation was confirmed by Sanger sequencing in and do not report functional assays or a change in treatment. We individual proteins;Downloaded at individual from Mendelian loci, approximately jama.ama-assn.org at Harvard University May 11,to2011 variants (SNVs) were detected usinga Samtools a licensed clinical laboratory. Functional demonstrated an inreportinthe whole exome on sequencing reach clinical (13) and further 85% of the disease-causingassays mutations can typically be found theuse of (see Methods). For heterozygote creased susceptibility to activation-induced cell death and defective diagnosis alter treatment in a single child with acalls life-we required at least coding region or in canonical splice sites (1). For complex traits,and filtered coverageundefined by reads form with of different start sites, base call with responsiveness to NOD2 ligands, consistent with loss of normal previously inflammatory genome-wide association studies have identified morethreatening than 250 but10! 7 Phred-like quality266600]). scores greater than 45, and the probability X-linked inhibitor of apoptosis protein function in apoptosis and NOD2 bowel disease (IBD) (AHC(14) [OMIM# common variants associated with risk alleles that contribute to a signaling. Conclusions: Based on this medical history, genetic and frequency of major and minor Thesmall patient of is athe male who initially presented at 15 alleles monthsdeviating from the wide range of diseases (2, 3). To date, most of these impart "7 functional data, the child was diagnosed as having an X-linked inhibitor . Rare SNVs that cluster within binomial of atabscess. least 10 The poor weight gain distribution and a perianal abscess effects on disease risk (e.g., odds ratio of 1.2); moreover, with even when of apoptosis deficiency. Based on this finding, an allogeneic hemato1 kb were tagged and evaluated for mapping enlarged,ofdrained spontaneously, but failed to close despite errors. SNVs were extremely large studies have been performed, the vast majority poietic progenitor cell transplant was performed to prevent the develfor effect on the encoded proteinHe and for conservation several roundsannotated of oral, and then parenteral, antibiotics. the genetic contribution to disease risk remain unexplained (4–6). opment of life-threatening hemophagocytic lymphohistiocytosis, in by comparison versus sequences of 43 vertebrate species (15) and subsequently These findings suggest that individually rare variants with relatively developed diarrhea and weight loss, despite supconcordance with the recommended treatment for X-linked inhibitor of orthologues and worm (see Methods). plemental enteral feedings, in andflyhis condition continued to de-
G
2
O
large effect may account for a large fraction of this missing trait teriorate over a period of 6 months, with referral to our hospital variance. Indeed, studies addressing this question have documented at 30 effect months. He had a weight of 8.1 kg, length 81.2 cm, and the presence of individually rare variants with relatively large
Downloaded from jama.ama-assn.org at Harvard University on April 26, 2011
Author contributions: M.C., U.I.S., S.M., and R.P.L. designed research; M.C., U.I.S., W.J., T.L., From the 1Human and Molecular Genetics Center; 2The Department of body mass of 12.7 (all "3¨.,percentile), indicating severe 8). Consistent the Mendelian coding variants have index I.R.T., P.Z., A.N., A.B., S.O S.S., C.N.-W., A.F., S.M., and R.P.L. performed research; M.C., Pediatrics, The(7, Medical College of with Wisconsin, Milwaukee; 3model, The Children’s stunting and malnutrition. Examination anesthesia 4 U.I.S., W.J., and R.P.L. analyzed under data; and M.C., U.I.S., showed W.J., and R.P.L. wrote the paper. proven to be prevalent sources of such rare variants. Hospital of Wisconsin, Wauwatosa, Wisconsin; Molecular Diagnostic Lab5 fistulaeThe and deepdeclare fissures. Initial endoscopy showed a oratory, Greenwood Genetic Clinic, Greenwood, South Carolina; The De- of perineal authors no conflict of interest. These considerations motivate implementation robust appartment of Surgery; andto6The Department of Physiology, Medical rectal (i.e., stricture Freely and available linear online ulcersthrough of the proaches sequencing complete codingThe regions of genomes the rectum; PNAS openthe accesssigmoid option. College of Wisconsin, Milwaukee, Wisconsin. colon and proximal bowel were healthy. Biopsy showed focal 1
the ‘‘exome’’). This has the potential to play a major role in disease
Integration Proposal for Genomic Pathology
To whom correspondence should be addressed. E-mail:
[email protected].
active proctitisThis with ulceration. The child was treated with Elizabeth A. Worthey, PhD, Human Molecular Genetics and the gene discovery andandalso in clinical useCenter for establishing a genetic article contains supporting information online at www.pnas.org/cgi/content/full/ Department ofdiagnosis. Pediatrics, The of Wisconsin, 8701 Watertown nasoenteric and infiximab for a presumptive diagnosis of 0910672106/DCSupplemental. AsMedical codingCollege regions constitute only approximately 1% of feeds Plank Road, Milwaukee, WI 53226. E-mail:
[email protected]. Crohn disease. Disclosure: The authors declare no conflict of interest.
Despite treatment, the perineal fistulae persisted, and new ones developed threatening the scrotum.www.pnas.org"cgi"doi"10.1073"pnas.0910672106 A diverting sigmoid colostomy was performed to divert fecal material and facilitate fistulae closure. The colostomy and mucus fistula failed to incorporate, and new fistulae developed. Although the perianal fistula and the mucosa of the defunctionalized distal limb recovered, the afferent limb became inflamed, eventually involving the entire colon, but not the terminal ileum or upper gastrointestinal (GI) tract. The patient was started on long-term total parenteral nutrition using a peripherally inserted central
19096 –19101 ! PNAS ! November 10, 2009 ! vol. 106 ! no. 45
Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal’s Web site (www.geneticsinmedicine.org). The first two authors contributed equally to this work. Submitted for publication August 12, 2010. Accepted for publication November 23, 2010. Published online ahead of print December 17, 2010. DOI: 10.1097/GIM.0b013e3182088158
Genetics
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Physician sends sample to Pathology (blood/tissue)
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Pathologists
Personalized Risk Prediction, Medication Dosing, Diagnosis/ Prognosis
Dec 18, 2018
Why Pathologists? We have access, we know testing
Access to patient’s genome
Just another laboratory test
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Integration Proposal for Genomic Pathology
100K Genomes Project
• Integration of relevant pathological findings (morphology, expression and genetic profile) for: • Better understanding (Pathobiology – Diagnosis) • Future evolution (Prognosis) • Directing treatment options (Prediction) • Integration ≠ Addition • Integration incorporates interactions
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Integrating Information for the Care of Solid Neoplasms
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Cancer Treatment: NGS of Tumor
5 Jones SJM, et al. Genome Biol. 2010;11:R82
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• 78-year old male • Poorly differentiated papillary adenocarcinoma of tongue • Metastatic to lymph nodes • Failed chemotherapy • Decision to use nextgeneration sequencing methods
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Case History
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Methods and Results
100K Genomes Project
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• Analysis • Whole genome • Transcriptome • Findings • Upregulation of RET oncogene • Downregulation of PTEN
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X
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1 month pre-anti-RET
Integration Proposal for Genomic Pathology
Anti-RET added
1 month on anti-Ret
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X
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Would like to identify tumor, know prognosis, treatment options
Integration Proposal for Genomic Pathology
100K Genomes Project
Pathologists
Personalized Tumor Treatment Plan
Dec 18, 2018
Why Pathologists? We have access, we know testing
Access to tumor genome 10
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100K Genomes Project
• Conventional pathology • Evaluation of tumor cells, microenvironments, and inflammatory response • Dynamic process of tumor progression at: • Invasion capacity for intraepithelial lesions • Metastatic capacity for invasive lesions • Genomic aspect • Gene expression levels • Genetic interactions • Structural changes (sequence, copy number) including expected cellular impact (low, moderate, severe)
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Integration Layers
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• Heritable genomic targets • Does not change during lifetime
• Pathology Clues • Multicentricity • Histological features • Perilesional tissue reaction
• Familial tumor syndromes are good models due to: • Synchronic and metachronic tumors • Range of precursor lesions and established neoplasms are frequent
Integration Proposal for Genomic Pathology
100K Genomes Project
• Germline
Dec • 18, Dec 18, 2018 2018
What we could test for – Integrated approach
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Inflammation and Cancer
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Inflammation and Cancer
14 Science. 2006 Sep 29;313(5795):1960-4. Galon J et al. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome.
Integration Proposal for Genomic Pathology
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Int J Mol Sci. 2015 Apr 17;16(4):8655-75. doi: 10.3390/ ijms16048655. Diaz-Cano SJ. Pathological bases for a robust application of cancer molecular classification. Int J Mol Sci. 2012;13(2):1951-2011. doi: 10.3390/ ijms13021951. Epub 2012 Feb 13. Diaz-Cano SJ. Tumor heterogeneity: mechanisms and bases for a reliable application of molecular marker design. Histopathology. 2008 Jul;53(1):1-19. doi: 10.1111/j. 1365-2559.2007.02937.x. Epub 2008 Feb 12. Diaz-Cano SJ. General morphological and biological features of neoplasms: integration of molecular findings.
Arreste d CC
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Proliferating CC
HH, PDGF
CSF-1, IL-1β
Polynucl
Mononucl
EGF
Cancer Stem Cell (CSC)
DC
Invasive CC
HGF
Proteases
TA Macrophage
Cyto- & Chemokines (CXCL12, IL-1β)
FGF2 VEGF
TGF-β
Proteases
VEGF
s ell lc lia es e t oth icy do er En & p
MDSC
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Integration Proposal for Genomic Pathology
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Competition AC C
AC C
AC C AC C
PCC PCC
PCC
Amensalism
Commensalism AC C
ICC ICC
CSC
ICC
CSC CSC
CSC
PCC
Mutualism
PCC
Parasitism ICC
PCC AC C ICC CSC
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CSC
Predation
ICC
Int J Mol Sci. 2015 Apr 17;16(4):8655-75. doi: 10.3390/ijms16048655. Diaz-Cano SJ. Pathological bases for a robust application of cancer molecular classification. Int J Mol Sci. 2012;13(2):1951-2011. doi: 10.3390/ijms13021951. Epub 2012 Feb 13. Diaz-Cano SJ. Tumor heterogeneity: mechanisms and bases for a reliable application of molecular marker design. Histopathology. 2008 Jul;53(1):1-19. doi: 10.1111/j.1365-2559.2007.02937.x. Epub 2008 Feb 12. Diaz-Cano SJ. General morphological and biological features of neoplasms: integration of molecular findings.
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Mutational Signatures in Cancer
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100K Genomes Project
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The contributions of mutational signatures to individual cancers of selected cancer types.
Nature. 2013 Aug 22;500(7463):415-21. doi: 10.1038/nature12477. Epub 2013 Aug 14. LB Alexandrov et al. Signatures of mutational processes in human cancer
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Mutational Signatures by Cancer Subtype
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The prevalence of somatic mutations across human cancer types.
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• Analyzed 8,101 genes on chip microarrays • Reference= pooled cell lines • Breast cancer subgroups
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Dec 18, 2018
Nature. 2013 Aug 22;500(7463):415-21. doi: 10.1038/nature12477. Epub 2013 Aug 14. LB Alexandrov et al. Signatures of mutational processes in human cancer
22 Perou CM, et al. Nature. 2000; 406, 747
Integration Proposal for Genomic Pathology
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100K Genomes Project
Dec 18, 2018
General pathology evaluation of core variables:
Stratification by Cumulative Feature Acquisition:
Dec 18, 2018
Stepwise genomic analysis: Categorization by acquired capabilities Genetic impact of the alteration Mutational load Interactions
100K Genomes Project
Grading (low/high) Invasion (pushing/infiltrative) Extension (organ-confined or not) Lymphovascular and perineural invasion Necrosis (confluent or not)
Pathology Genomic Combined
Proposed Approach Systematic, general, by domains of knowledge Integration and simplification for better understanding
Integration Proposal for Genomic Pathology
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