EFTA01140242.pdf

Personalized genomic disease risk of volunteers Manuel L. Gonzalez-Garay'', Amy L. McGuireb, Stacey Pereirab, and C. Thomas Casket' 'Center for Molecular Imaging, Division of Genomia and Bioinformatics, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030; and ', Center for Medical Ethics and Health Policy, Department of Medicine and Medical Ethics, and 'Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 Contributed by C. Thomas Caskey, August 27, 2013 (sent for review July 11, 2013) Next-generation sequencing (NGS) Is commonly used for Results researching the causes of genetic disorders. However, its useful- Categories of Variants to Report to Patients. Variants obtained ness in clinical practice for medical diagnosis is in early de- from our workflow (described in Fig, 1) were reported using velopment. In this report, we demonstrate the value of NGS for three categories. Our first variant category consists of variants genetic risk assessment and evaluate the limitations and barriers identified in an individual where the alleles are found in Human for the adoption of this technology into medical practice. We Genome Mutation Database (HGMD) (13, 14) and labeled performed whole exome sequencing (WES) on 81 volunteers, and disease-causing mutations (DM). These alleles also were re- for each volunteer, we requested personal medical histories, quired to be rare (<1% allele frequency in 6,500 exomes from constructed a three-generation pedigree, and required their the National Heart, Lung, and Blood Institute (NHLBI) Exome participation in a comprehensive educational program. We lim- Sequencing Project (15) and the 1,000 Genomes Project ited our clinical reporting to disease risks based on only rare Genomes (16, 17)] and predicted to be damaging to protein damaging mutations and known pathogenic variations in genes function by two of three predictions algorithms [Polyphen 2.0 previously reported to be associated with human disorders. We (18), Sift (19-24), and MutationTaster (25)] using Database of identified 271 recessive risk alleles (214 genes), 126 dominant risk Human Non-synonymous SNVs and their functional predictions alleles (101 genes), and 3 X-recessive risk alleles (3 genes). We and annotations (dbNSFP) (26) as described in Fig. 2. The genome linked personal disease histories with causative disease genes in sequence data of each volunteer were reviewed and interpreted, 18 volunteers. Furthermore, by incorporating family histories into taking into account personal medical history, a three-generation our genetic analyses, we identified an additional five heritable pedigree with family history of diseases, and bioinformatics diseases. Traditional genetic counseling and disease education analysis. The medical history of each volunteer in this cohort was were provided in verbal and written reports to all volunteers. Our rich with detail because each had a private physician used for report demonstrates that when genome results are carefully annual examinations, and in some cases. disease therapy. Fig. 3 interpreted and integrated with an individual's medical records summarizes the results of our pipeline: we recruited 81 non- and pedigree data, NGS is a valuable diagnostic tool for genetic related volunteers and sequenced their genomic DNA using disease risk. exome sequencing. We detected 65,582 unique nonsyttonymous coding variants (nscv). Every nscv was interrogated for human molecular medicine I disease prediction I whole exome sequencing inherited disease mutations using the HGMD (13, 14) database from Biobase (DM category consisting of 109,708 variations). We were able to detect 1,036 HGMD (13, 14) DM variations. S equencing the whole genome of patients with genetic dis- orders has become reality since the sequencing of the first individual human in 2007 (1). Further advances in massively After using the filters described in Fig. 2, the number was reduced to 275 pathogenic variants. We identified in our cohort 208 au- tosomal recessive (AR) alleles (169 genes), 64 autosomal domi- parallel DNA sequencing are reducing the price of sequencing nant (AD) alleles (44 genes), and three X-linked recessive (XLR) an entire genome or exome. The quality and speed of sequencing and analyzing a personal genome are improving at an unprece- Significance dented pace, making possible the introduction of next-generation sequencing (NGS) into the clinic on a research basis (2-7). Replacing traditional methods for genetic testing of inheritable Advancements in NOS have stimulated international research disorders with next-generation sequencing (NGS) will reduce initiatives to identify genetic links to rare disorders in children, the cost of genetic testing and increase the information avail- with an average diagnostic success of 20-25% and the discovery able for the patients. NGS will become an invaluable resource of new disease-gene associations (8-12). for the patient and physicians, especially if the sequencing in- The rapidly increasing number of aging adults in our society formation is stored properly and reanalyzed as bioinformatics will place unprecedented demands on the health care system. To tools and annotations improve. NGS is still at the early stages provide adults with a healthy longevity we need to develop of development and it is full of false-positive and -negative a system to identify genetic risk and apply early intervention on results and requires infrastructure and specialized personnel to pathology progression. In this report, we decided to sequence the properly analyze the results. This paper will explain our expe- whole exomes of a healthy adult cohort of 81 volunteers and rience with an adult population, our bioinformatics analysis, evaluate the value of applying NOS in combination with medical and our clinical decisions to assure that our genetic diagnostics history and pedigree data. In this report we plan to address three were accurate to detect carrier status and serious medical main questions. (i) What genetic discoveries need to be provided conditions in our volunteers. to the volunteers? (ii) What is the practical value of delivering this information to volunteers? (iii) What are the challenges and Author contributions: m I.G.-0. and CT.C. designed research; PAL.G.4 . A LM.. 5.P.. and barriers to the adoption of this powerful technology into medical CT.C. performed research; PA.L.G.4. analysed data; and M.LGA...A.L.M. S.P. and CT.C. practice? mote the paper. The individual genetic reports yield helpful medical risk in- The authors declare no conflict of Interest. formation, suggesting that population sequencing of asymptom- Freely available online through the PNAS open access option. atic adults may prove to be valuable and useful. We provided to 'To whom correspondence may be addressed. E-mail: manuell.GonzalezGarayeluth,unc. the participants, under our institutional review board, genetic edu or tcaskeyelbotedu. risk findings from the analyses and genetic counseling to discuss This article contains supporting information online at vninv.pnas.orgiloalcupisuppildoi:10. their results. 1073/Dna 13159341IONIXTv0Plementet www.yroas.orgrcgikloill0.10734mas.1315936110 PNAS Earty Edition I 1of 6 EFTA01140242  physicians for further analytes measurements. There were two IINININOISNONInC• individuals with morbid obesity (body mass index of 32 and 37 kghto who carried an MC4R allele associated with pediatric NovoMen moNnint la enlocenot MIN Went+ meow,: SAPAtesb/Picard obesity and rare heterozygotic adults (35, 36). Two ophthalmo- SAMMe .Remove duplicate logic disease/gene associations were identified. The childhood •Rnallbrate aligrenents GAN brittle corneal syndrome type 1 occurred in a volunteer who had •local rtalignmnits undergone successful corneal transplant and carried a putative compound heterozygosity in ZNF469 (37). One volunteer was GAIN% Bantian under care for macular dystrophy and carried an ABCA4 allele a c" dance SNIVIndel taller (38). One sterile male volunteer was found to have an insertion %N s in gene USP26 (known to be responsible for infertility in men) SNM annotated sciostindels a IMoons Welt Cereal° deournamoon (39). Associations for melanoma and breast cancer were identi- uwEll fied. The two patients with melanoma carried different gene ANNMAR allele associations: GRIN2A and BAG4 (40-42). Two volunteers diagnosed with breast cancer had different allele associations in Hg. 1. Workflow for processing NGS data. Raw sequencing data are aligned BRCA2 (43, 44). Single cases of early onset prostate (LRP2) (45) against the reference sequence using Novoalign software from NovoCraft. and follicular thyroid cancer (TPR) cancer were identified (46, SAM files are preprocessed using SAMtoots and Picard to create BAM files and 47). A volunteer with nonsyndromic deafness was found to have remove duplicates. The Genome Analysis Tcolkit (GATK) is then used to recalibrate the alignments, perform local realignments, and identify SNPs and risk alleles in two genes associated with autosomal dominant indels. Finally, SnpEff and ANNOVAR are used to annotate variants. (AD) deafness and had a three-generation positive family history of deafness (48). In each case, the volunteer was instructed to inform their Physician and was requested to confirm the ge- alleles (3 genes). These data resulted in an average of 3.5 disease nomic allele identification in a Clinical Laboratory Improve- allele reports per volunteer. ment Amendments (CLIA)-certified laboratory, even when each The approach for a second category of variants consisted of reported allele had been sequenced twice in independent studies. creating a personalized list of candidate genes from Online The finding provided information for personal and family risk Mendelian Inheritance in Man (OMIM) (27, 28) known to be counseling not possible before gene association. associated with the disorders reported in the medical literature. Incorporation of Three•Generation Pedigrees into the Genetic Analyses. We detected 131 alleles (131 genes) using this approach. Each one of these variants provided a potential causation for the volunteer's The three-generation pedigree medical information was analyzed disorders. Each one of the variations obtained from this approach to identify those volunteer families who warranted additional ge- passed our stringent pipeline. This approach added on average netic study. Table S2 lists those genetic disorders identified by another 2.0 disease alleles per volunteer report. pedigree/familial medical history. In each case, the volunteer was The third approach used a family history to create a person- counseled for the family risk and encouraged to contact at risk alized list of candidate genes from OMIM (27, 28). and as be- family members who may benefit from focused genetic studies. fore, we compared our list of candidate genes with the disorders Three of the families have reported that they have had their fa- reported in the family history. milial genetic diagnosis resolved at this time paraganglioma (49), Before reporting an allele to the volunteer, we reviewed the Prader-Willi syndrome (50, 51), and ankylosing spondylitis (AS) original publications that support the pathogenicity of all of the (52)1. One additional family is under study rourette syndrome alleles (HGMD) and/or the evidence associating the gene with (534 Additional familial disease risks were identified by history the disorder (OMIM). At this time, all three abovementioned for atrial fibrillation (AR), bicuspid aortic valve (BAV), dyslexia categories of investigation were reported in full recognition; (AR), Fatny's (XLR), gall stones (AD), and myotonic dystrophy some would be found to be non-disuse-producing alleles as (anticipation AD). Success with this approach was productive but databases improve and functional assays complement informatics not universally accepted because disease/gene resolution requires predictions. We have updated clinical reports as these data interaction with interested and motivated family members. emerged and counseled the patients on the options for reducing or eliminating the disease risk. WWICall Rant NM 1 Sam Ms Disease Genes Identified in the Cohort. Table SI summarizes our dOSNP 132 CGI var.annosadonFie disease associations. Matching personal medical records to per- sonal genome reports was informative. We elected to report ,0. GamretSess brown Gene OK%) findings as disease-gene associations instead of reporting findings as diagnostic because we did not included in our study traditional mpgfl LANNCNAR (na-toding vatianta) "surrogate markers" (analytes, proteins, and imaging) for the 4 Stank:IKIND Db foe (Mum, Cause* Mutations confirmation of a disease diagnosis. We considered potentially 1% Aker Out variants MM >r causative findings to be those mutations that are predicted to be n Should have been convect damaging for damaging in addition to being reported in either HGMD (13, 14) menu 2/3 ptecutions tools .11 or OMIM (27, 28) databases. These mutations are considered to . frolyphen-2. Sift and hivtatronTaster1 be "need to know" and are reported to volunteers. There was Sternalfrequencyfilter < 3% identification of associations for vascular disease and/or hyper- cholesterolemia in five individuals related to LDL receptor YPOVarlards Won (LDLR) alleles. LDLR mutations are causative of early onset Fig. 2. Pipeline to generate variants reports. Every variant in the variant call autosomal dominant coronary artery disease (CAD) and manifest format file is annotated using spnEff and ANNOVAR; nonsynonymous cod- hypercholesterolemia (29, 30). Three individuals were taking ing variants are annotated using the commercial version of the HGMD da- statins related to their hypercholesterolemia. Two individuals tabase. (Left) Our selection of variants by the creation of a personalized were not under care but had history of personal hypercholester- candidate gene list using medical history and family history for each vol- olemia and in one case a son with hypercholesterolemia. unteer. Mutations with a minor allele frequency of >1% are removed using There were four volunteers detected with risk genes for di- frequencies from the NHLSI exome sequencing project (ESP), 1,000 Genomes abetes mellitus (31-34). Two of the individuals were under Project. Variants that are consider benign by two of three predictions tools therapy for diabetes 2, whereas two additional volunteers had are removed (using dbNSFP). Finally, we remove variants that are present in elevated fasting blood sugars and were being followed by their our cohort more than three times. 2 of 6 I www.pnas.orgfcgikloW10.10734mas.1315934110 Gonzalez-Garay et al. EFTA01140243  81volunteers 65,582 NSCV NSC-snps Exon Sequencing Using HGMD (109,708 annotated 1,036 NSC-sts from HGMD variants) A 275 NSC-snps from HGMD after filtering 160 NSC•snps from OMIM Medical and family History Interpretation ck.1 Medical History Family History Negative History B B 206 HGMD Autosomal recessive (169 Genes) 23 disease-gene 4 resolved 63 MAIM (No.HGMD)Autosemal recessive (63 Genes) associations 1In progress 3 HGMD X linked recessive (3 Genes) 6 OMIM (No-HGMD) X linked recessive (6 Genes) 64 HGMD Autosomal Dominant (44 Genes) 62 °Mill (tio.HGIND)AulosoM31Dominant (62 Genes) Fig. 3. Summary of result. The flowchart provides the number of variants from each step of the pipeline described in Fig. 2. Table S3 provides a sampling of the recessive risk alleles. They BRCAI, BRCAZ PALB2, R4D5IC, and RADS& Two volunteers constitute the majority of the observed alleles. Of the 160 off- with BRCA2 risk alleles were diagnosed with breast cancer. One spring of the 81 volunteers, no children were affected with these man carried a premature chain termination mutation and has disorders. MI volunteers indicated their families were complete, a first-degree relative with breast cancer (50s). A third volunteer and thus, no spousal genetic studies were recommended, but had a frame shift mutation (high-risk allele) but not found to information was proposed to be provided to reproductive age have breast cancer. All alleles were predicted to be damaging. descendants. Many of the genes identified are pan of prenatal Eight volunteers had first-degree relatives with breast cancer, carrier screens and/or newborn state-sponsored screening pro- whereas four had a negative family history of disease. All were grams [phenylketonuria, maple syrup urine disease, cystic fibro- advised to seek confirmation via a CLIA-cenified laboratory. sis, Niemann-Pick disease, Gaucher disease, factor V Leiden One patient with an HGMD (13, 14) allele was confirmed but thrombophilia, medium-chain acyl-CoA dehydrogenase (MCAD) predicted to be "neutral" by a commercial laboratory. All were deficiency]. Undoubtedly, NGS will expand the number of non- counseled regarding the need for regular mammograms and unreported disease alleles and scope of genes studied for couples gynecological examinations and were requested to inform their in the pregnancy setting. The Beyond Batten Disease Foundation physician of this research risk allele identification. of Austin, TX (54), has this goal. Table S6 displays the colon cancer alleles. There was no disease Table S4 shows that a category of high concern was the incidence of colon cancer in this group with the exception of one identification of XLR disease risk alleles among our female vol- volunteer with a positive dysplastic polyp biopsy. Five volunteers unteers. One volunteer had an affected son (isolated case) with had a positive family history of colon cancer. Five volunteers had Fabry disease that was diagnosed before our study. There were no family history of disease. All were advised to obtain confir- four disease alleles identified, each listed in HGMD (13, 14). matory CLIA-certified laboratory diagnosis and advise their phy- There was no family history of these disorders found in the three- sician of the research allele identification. Of the 10 volunteers, generation pedigree of each. MI were counseled to have their test many had undergone colonoscopy as pan of their health care. confirmed and daughters studied in a CLIA-certified laboratory Table S7 includes all of the remaining type of cancers. Two given the high disease risk (50% for men). Three men in our study volunteers diagnosed with melanomas were found to have dif- had alleles predicted from the OMIM (27, 28) disease database to ferent disease gene risk alleles. We identified 10 volunteers with be causative for cutis laxus, Duchenne muscular dystrophy, con- prostate risk alleles. One volunteer reported a diagnosis of genital nystagmus, and hemophilia A, illustrating the challenge of prostate cancer at age 55 while the other nine volunteers predicting damaging mutations bioinformatically. None had the reported no familial history of the disease. Genetic counseling disorders. Counseling and family study were individualized for for cancer risk required the greatest counseling time. The con- each disease risk. Volunteers were made aware of database errors cepts of the two-hit hypothesis (55) and "somatic mutations" in the reports. (56) were difficult to grasp for the volunteers, even when we Tables S5-510 provide a third category that is very problem- discussed the subject in great detail during the education session. atic, the AD group. The allele identification is as previously All volunteers were provided information regarding standard of described, but counseling is more difficult because of variation in practice approaches for early detection of the respective cancer. severity and time onset. For this age group of volunteers, the Table S8 lists all of the affected volunteers with cardiomyop- interest was high because disease prevention was frequently athies (57). Five volunteers had a medical history of cardiac expressed as a goal in the face-to-face counseling meetings. A dysrhythmia with identified risk alleles. One younger (50s) vol- poststudy survey also reflected this objective. We focused in this unteer had first-degree relatives requiring pacemakers and car- paper on the three major causes of death in the United States: ried two risk alleles. Three volunteers had either stent placements cancer, cardiovascular disease, and neurodegenerative disease. or bypass procedures related to CAD. Each was in their 70s. In our analysis of each volunteer, we reviewed the genomic and Table S9 lists the 11 volunteers who had no apparent disease family data. but had a positive family history of tachycardia, sudden death, Table S5 lists the breast cancer risk results. There were 12 and CAD and carried risk alleles. We provide this experience to volunteers found to have breast cancer risk alleles of genes broaden alertness to both genetic causation and risk of disease Gonzalez-Garry et al. PNOS tarty Edition I 3 of 6 EFTA01140244 for adult-onset cardiovascular disease (58). Of the alleles listed and the 69 sets of whole genomes from CGI (15-17, 67). How- in Tables SE and S9, 13 alleles were found in HGMD (13, 14). ever, we need larger datasets from very carefully phenotyped We advised volunteers to inform their physicians of these results patients to assist in the interpretation of the variants in our for their long-term clinical care. patients. The million genome project of the US Department of In Table SI0, we listed the results for adult-onset neurodegen- Veterans Affairs (68) has the potential to provide such data, as erative diseases. Our findings were limited but of high interest to the well as private health plans considering adaptation of genome cohort. It was frequently asked by volunteers if they had Alz- sequencing. heimer's risk. We summarize our findings for Alzheimer's and Parkinson risk alleles (59, 60). The genes included APOE, APP, Genetic Discoveries Provided to Volunteers. There are several PSENI, MAPT, ElF461, GBA, GIGYF2, LRRIC.2, PARIC2, PM20DI, approaches to disclose the results to volunteers. Groups like and SNCA. There were nine volunteers with HGMD (13, 14) listed Patel et al. use the statistics and epidemiology approach in risk alleles. Of these, two had a positive family history of Parkinson reporting the polygenic risk assessment using common SNPs that disease and one with Alzheimer's disease. One of the PARK2 alleles have been previous associated with genetic disorders from ge- occurred in a volunteer who provided a history of three second- nome-wide association studies (69). The PGP-10 project uses an degree relatives in a sibship affected with disease. The reminder had automated tool or Genome Environment Trait Evidence (GET- no family history of either disease. There were 25 alleles predicted Evidence) system, with is a system that is collaboratively edited to be damaging. One is a frameshift allele. None of these volunteers (70). For this project, we decided to focus on reporting only high- had a family history of disease. quality variants that are rare in the population and considered damaging by two of three commonly used predictions algorithms. Discussion In addition, the variant has to be either reported in HGMD Exome Sequendng Is Limited. The full spectrum of disease muta- under category DM or the gene has to have been previous tion identification is not satisfied by exome sequencing alone associated with a genetic disorder (OMIM). The group of vol- because large deletions, copy number variations (CNVs), and unteers consisted of adults with complete medical and family triplet repeats are not reliably identified at this time. Further- history so we personalized the reports as described in Fig. 2 to more, exon capture relies on probe design. For example, the specifically try to identify molecular explanations for the mal- discovery of the MAGEL2 mutation in our Prader-Willi patient adies reported in their medical or family history. This approach was made using whole genome sequencing (WGS) from com- generated reports that were easy to explain and accepted by the plete genomics and missed by exome capture because of high GC patients during the genetic counseling session. content (51). The accuracy of coding allele identifications was. however, quite high and thus of great utility as a genome Medical Histories and Family Pedigrees Complement Sequencing screening approach. CGI (61) sequencing produced higher cov- Resift. The utility of genome data was significantly enhanced erage than exome sequencing data for CNV, large deletions, when integrating standard medical care features of personal and and regulatory elements will have utility as we analyze previously family disease diagnosis. The significant number of 23 disease labeled "junk" DNA for disease causation (62). There is also the associations in all likelihood represents a bias of our volunteers issue of our limited knowledge of disease alleles within the to seek answers to their personal disease history. This observa- databases. One of our biggest challenges for the interpretation of tion may hold a key to how we obtain maximal use of genome human genomes is the lack of gene annotations and the errors in sequencing--sequence the disease index cases. Our experience databases. Our knowledge base for human disorders is small. would suggest a high value for that utilization. This approach has There are only —100,000 pathogenic variants in the HGMD (13, been clearly documented to be successful for pediatric genetic 14) database and a fraction of them have errors. If we do not use disorders but not exploited for adult-onset disease. The practical annotated variants but instead gene annotations as our source of value of this study is summarized in Tables SI and S2 and fell information, we can calculate the fraction of knowledge that we into two general categories: (i) new knowledge of the genetic risk can use at this time. For example, the number of genes associ- and heritability for themselves and family; and (ii) options for ated with human disorders reported by HGMD (13, 14), OMIM therapy (CAD) or imaging (cancer) for personal and extended (27, 28), UniProtICB (63), Gene Atlas (64), etc. is 4,622. From family care. By using the medical and family history, we were the 4,622 genes, only 1,955 genes have high-quality data because able to clarify the genetic risk in 6 of the 81 cases. One of the they are part of the GeneTest (65) database. GeneTest (65) is cases yielded a new discovery of a gene associated with Prader- a database originally created by the National Center for Bio- Willi syndrome. which is described in another paper (51). technology Information to track all of the laboratories worldwide that offer a genetic test for a gene. With this information, we Prenatal vs. Adult Genetic Screening. The technology and this report know that the fraction of genes that we can use for the in- beg the question of whether we are prepared to offer adult disease terpretation of a human genome of a successful high-quality risk screening. Currently, prenatal and newborn screening for whole exome or whole genome dataset is -7-18% when using a selected set of frequently occurring disease alleles (not genome the high confidence set of 1,955 genes or a set of 4,622 genes. sequencing) is a standard of practice. There are questions that Despite these limitations, this report documents the utility for deserve medical and ethical review before adult screening disease associations and risk. becomes a standard of practice. First, for reproductive and new- During the last few years, the field of NOS has developed born diagnosis, typically only actionable childhood diseases are a large number of tools that make it easier to handle the analysis explored, which respects the future autonomy of the child and of reads, variant calling, functional prediction, and annotation preserves her right to an open future (71, 72). Because adult (66). There are also large publicly available datasets of healthy screening decisions would be made by an autonomous individual individuals that can be used as controls that can be used to for her own health decisions, broader conceptions of utility, in- remove technology specific errors or filter out common poly- cluding personal utility, need to be considered (73). It is a clear morphisms. As we begin to use whole genome sequencing at an and simple decision to provide patients with actionable genetic increasing depth, we are discovering more variants, so these information from a WES study; on the other hand, it is challenging public datasets are becoming increasingly important for quality and it raises a difficult ethical question to decide what to do with control and filtering of variants in smaller projects. One of the incidental genetic findings that are not actionable and could lead main limitations is the lack of access to public and private ge- to physiological distress to the patient (e.g. APO-E for Alzheimer nome and exome variants. There are thousands of datasets, but dictate). Despite this ethical dilemma our group of volunteers the majority are inaccessible to the scientific community. We elected to receive information even if the genetic information recognize the existence of the 1,000 Genomes project, the might not be actionable. Only 3% of the volunteers were uncertain NHLBI Exome Sequencing Project (ESP), Exome variant server, about receiving nonactionable information (SIPausnuly Survey). 4 of 6 I www.pnas.orglegildoi/10.10734wias.13I5934110 Gotualez-Garay et al. EFTA01140245 Volunteer Response to Clinical Reports. From our poststudy survey, technology and cost. Bioinformatics focused on the practical ex- we found that 72% of the responders reported speaking with traction of medical relevant/actionable data are a challenge. We their physician about their results. This raises important ques- relied heavily on HGMD alleles for "need to know" information tions about whether nongeneticists are adequately prepared to to patients. This approach is flawed in three ways: (i) databases counsel patients based on WES results and whether such follow- contain errors; (ii) highly validated disease databases are scattered, up will lead to iatrogenic harm or unjustified use of health care private, and limited; and (iii) the future will provide more disease resources (74). Twenty-five percent reported changing their risk alleles by sequencing than by patient reports in the literature. behaviors because of the results, which is surprising given that Our current limitation for interpretation of a genome is not the previous reports found no significant behavior change resulting quality of the data of the coverage of the genome but our disease from adult risk screening in a direct-to-consumer setting (75). knowledge database. R. Cotton's Human Variome Project (62) Despite that all of the participants were clearly informed that together with Beijing Genome Institute are proposing to create their results originated from two independent sequencing experi- a highly validated disease allele database. ments and that we advised them to have their results clinically New technological advances such as structure-based pre- validated in a CLIA-certified laboratory, 78% reported that they diction of protein-protein interactions on a genome wide scale did not have the results confirmed. This low percentage of (80), 3D structure of protein active and contact sites (SI), high- confirmatory results from the volunteers raises the question of throughput functional assays of damaging alleles (81-83), and whether it is sufficient to counsel research participants to have new approaches that combine analytes, metabolomics and ge- results clinically confirmed or if investigators should be required netic information from a single individual (84) are just a few to confirm results before disclosure. examples of the new technologies that will help us to generate It was apparent for some volunteers that they were seeking better interpretation of genomic data. information related to familial diseases. Resolution of these The delivery of the genome risk information will need to be questions required family member interest and motivation be- carried out by a new cadre of physicians and counselors skilled in cause, in all cases, we had sequenced the nonrisk family mem- medicine, genetics, and education/counseling. These experts will ber. We followed up each case with a referral to a qualified need to integrate into medical care as well as has been done for genetics program with diagnostic capacity for the suspected newborn screening, prenatal diagnosis, and newborn genetic genetic disease. disease diagnosis. Our efforts to analyze cancer, cardiovascular, neurodegener- The approach of adult screening is in its early phase but from ative, and obesity/diabetes risk were successful but needed con- our data appears very promising. We conclude that the genomic siderable education/counseling to avoid confusion over risk vs. study of adults deserves intensified effort to determine if "need diagnosis. Second, there are standard of care options for those to know" genome information has the utility for improved with risk alleles for cancer, cardiovascular disease, and diabetes quality of health for our aging population. for disease modification or early diagnosis. 'Thus, sequencing serves as a new screening risk detection approach toward the Materials and Methods objective of improved health. It is expected that genomic studies The oversight of this research was under two institutional review boards: (i) will increase surveillance studies (e.g., colonoscopy. gynecologic HSC-IMM-08-0641 (University of Texas Health Science Center at Houston) examinations, mammograms, cardiovascular markers and scan- and (ii) H-30710 (Baylor College of Medicine). ning studies) but has the possibility of more precisely identifying the patients who may benefit from rlititsce prevention surveillance. Cohort Description. The cohort consists of members and spouses in the The area of adult-onset neurologic disorders is an increasing Houston Chapter of the Young President Organization (YPO) (85). Theentire concern worldwide as our population ages, thus exposing disease description of the cohort can be found in SI Materials and Methods. incidence not seen earlier. The genetic disease discoveries are limited. Confirmatory diagnostics such as image analysis and MS Sequencing. Standard NGS was performed using illumine HighSeq; an biomarkers/surrogate markers are just emerging, and prevention extended explanation can be found in Materials and Methods. therapeutic options are nonexistent. Although one might ques- tion the utility of screening for these disorders at this time, the Sequencing Analysis. Fig. 1 illustrates OUf pipeline, and fig. 2 describes our experience with Huntington disease (76) screening taught valu- pipeline to detect known pathogenic variations. Additional details can be able lessons on how to proceed with studying and counseling found in Sf Materials and Methods. families at risk. Furthermore, there are new therapeutic trials in disease prevention for Alzheimer's (58) and Parkinson disease Counseing. Genome counseling was conducted by a board-certified internist based on the genetic cause of disease. These clinical trials use and medical geneticist by both individual meetings and two written sum- genetic diagnosis to select participants, which is also a successful maries over a period of 12 mo. Additional information can be found in SI approach in cancer drug development (77-79). Materials and Methods. Barriers to the Adoption of Genetic Screening via Sequendng. Al- ACKNOWLEDGMENTS. This work was supported by the Cullen Foundation for Higher Education and the Governing Board of the Greater Houston though the above comments would present the case for the value of Community Foundation. The funding organizations made the awards to the adult genetic screening via whole genome sequencing, there are University of Texas Health Science Center at Houston and Baylor College of major issues to be addressed. In our opinion, the least is sequencing Medicine. C.T.C. was the principal investigator of both grants. 1. Lew S. et al. (2007) The diploid genome sequence of an individual human. 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