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Pinto E Vairo F, Kemppainen JL, Vitek CRR, Whalen DA, Kolbert KJ, Sikkink KJ, Kroc SA, Kruisselbrink T, Shupe GF, Knudson AK, Burke EM, Loftus EC, Bandel LA, Prochnow CA, Mulvihill LA, Thomas B, Gable DM, Graddy CB, Garzon GGM, Ekpoh IU, Porquera EMC, Fervenza FC, Hogan MC, El Ters M, Warrington KJ, Davis JM, Koster MJ, Orandi AB, Basiaga ML, Vella A, Kumar S, Creo AL, Lteif AN, Pittock ST, Tebben PJ, Abate EG, Joshi AY, Ristagno EH, Patnaik MS, Schimmenti LA, Dhamija R, Sabrowsky SM, Wierenga KJ, Keddis MT, Samadder NJJ, Presutti RJ, Robinson SI, Stephens MC, Roberts LR, Faubion WA, Driscoll SW, Wong-Kisiel LC, Selcen D, Flanagan EP, Ramanan VK, Jackson LM, Mauermann ML, Ortega VE, Anderson SA, Aoudia SL, Klee EW, McAllister TM, Lazaridis KN. Correction: Implementation of genomic medicine for rare disease in a tertiary healthcare system: Mayo Clinic Program for Rare and Undiagnosed Diseases (PRaUD). J Transl Med 2024; 22:400. [PMID: 38689323 PMCID: PMC11061992 DOI: 10.1186/s12967-024-05185-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Jennifer L Kemppainen
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Carolyn R Rohrer Vitek
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Denise A Whalen
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kayla J Kolbert
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kaitlin J Sikkink
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Sarah A Kroc
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Teresa Kruisselbrink
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Gabrielle F Shupe
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Alyssa K Knudson
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Elizabeth M Burke
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Elle C Loftus
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Lorelei A Bandel
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Lindsay A Mulvihill
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Dale M Gable
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Courtney B Graddy
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | | | - Idara U Ekpoh
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | | | | | - Marie C Hogan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Mireille El Ters
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - John M Davis
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | | | - Amir B Orandi
- Department of Pediatric Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Matthew L Basiaga
- Department of Pediatric Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Adrian Vella
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Seema Kumar
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ana L Creo
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Aida N Lteif
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Siobhan T Pittock
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Peter J Tebben
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Avni Y Joshi
- Division of Pediatric Allergy and Immunology, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth H Ristagno
- Division of Pediatric Infectious Diseases, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mrinal S Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Phoenix, AZ, USA
| | | | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA
| | - Mira T Keddis
- Division of Nephrology, Mayo Clinic, Scottsdale, AZ, USA
| | | | | | | | - Michael C Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, MN, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sherilyn W Driscoll
- Division of Pediatric Rehabilitation Medicine, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | | | - Duygu Selcen
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | - Victor E Ortega
- Division of Respiratory Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Sarah A Anderson
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Tammy M McAllister
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
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Pinto E Vairo F, Kemppainen JL, Vitek CRR, Whalen DA, Kolbert KJ, Sikkink KJ, Kroc SA, Kruisselbrink T, Shupe GF, Knudson AK, Burke EM, Loftus EC, Bandel LA, Prochnow CA, Mulvihill LA, Thomas B, Gable DM, Graddy CB, Garzon GGM, Ekpoh IU, Porquera EMC, Fervenza FC, Hogan MC, El Ters M, Warrington KJ, Davis JM, Koster MJ, Orandi AB, Basiaga ML, Vella A, Kumar S, Creo AL, Lteif AN, Pittock ST, Tebben PJ, Abate EG, Joshi AY, Ristagno EH, Patnaik MS, Schimmenti LA, Dhamija R, Sabrowsky SM, Wierenga KJ, Keddis MT, Samadder NJJ, Presutti RJ, Robinson SI, Stephens MC, Roberts LR, Faubion WA, Driscoll SW, Wong-Kisiel LC, Selcen D, Flanagan EP, Ramanan VK, Jackson LM, Mauermann ML, Ortega VE, Anderson SA, Aoudia SL, Klee EW, McAllister TM, Lazaridis KN. Implementation of genomic medicine for rare disease in a tertiary healthcare system: Mayo Clinic Program for Rare and Undiagnosed Diseases (PRaUD). J Transl Med 2023; 21:410. [PMID: 37353797 PMCID: PMC10288779 DOI: 10.1186/s12967-023-04183-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/05/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND In the United States, rare disease (RD) is defined as a condition that affects fewer than 200,000 individuals. Collectively, RD affects an estimated 30 million Americans. A significant portion of RD has an underlying genetic cause; however, this may go undiagnosed. To better serve these patients, the Mayo Clinic Program for Rare and Undiagnosed Diseases (PRaUD) was created under the auspices of the Center for Individualized Medicine (CIM) aiming to integrate genomics into subspecialty practice including targeted genetic testing, research, and education. METHODS Patients were identified by subspecialty healthcare providers from 11 clinical divisions/departments. Targeted multi-gene panels or custom exome/genome-based panels were utilized. To support the goals of PRaUD, a new clinical service model, the Genetic Testing and Counseling (GTAC) unit, was established to improve access and increase efficiency for genetic test facilitation. The GTAC unit includes genetic counselors, genetic counseling assistants, genetic nurses, and a medical geneticist. Patients receive abbreviated point-of-care genetic counseling and testing through a partnership with subspecialty providers. RESULTS Implementation of PRaUD began in 2018 and GTAC unit launched in 2020 to support program expansion. Currently, 29 RD clinical indications are included in 11 specialty divisions/departments with over 142 referring providers. To date, 1152 patients have been evaluated with an overall solved or likely solved rate of 17.5% and as high as 66.7% depending on the phenotype. Noteworthy, 42.7% of the solved or likely solved patients underwent changes in medical management and outcome based on genetic test results. CONCLUSION Implementation of PRaUD and GTAC have enabled subspecialty practices advance expertise in RD where genetic counselors have not historically been embedded in practice. Democratizing access to genetic testing and counseling can broaden the reach of patients with RD and increase the diagnostic yield of such indications leading to better medical management as well as expanding research opportunities.
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Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Jennifer L Kemppainen
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Carolyn R Rohrer Vitek
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Denise A Whalen
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kayla J Kolbert
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kaitlin J Sikkink
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Sarah A Kroc
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Teresa Kruisselbrink
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Gabrielle F Shupe
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Alyssa K Knudson
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Elizabeth M Burke
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Elle C Loftus
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Lorelei A Bandel
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Lindsay A Mulvihill
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Dale M Gable
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Courtney B Graddy
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | | | - Idara U Ekpoh
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | | | | | - Marie C Hogan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Mireille El Ters
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - John M Davis
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | | | - Amir B Orandi
- Department of Pediatric Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Matthew L Basiaga
- Department of Pediatric Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Adrian Vella
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Seema Kumar
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ana L Creo
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Aida N Lteif
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Siobhan T Pittock
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Peter J Tebben
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Avni Y Joshi
- Division of Pediatric Allergy and Immunology, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth H Ristagno
- Division of Pediatric Infectious Diseases, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mrinal S Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Phoenix, AZ, USA
| | | | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA
| | - Mira T Keddis
- Division of Nephrology, Mayo Clinic, Scottsdale, AZ, USA
| | | | | | | | - Michael C Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, MN, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sherilyn W Driscoll
- Division of Pediatric Rehabilitation Medicine, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | | | - Duygu Selcen
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | - Victor E Ortega
- Division of Respiratory Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Sarah A Anderson
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Tammy M McAllister
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
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Chen X, Meyer MA, Kemppainen JL, Horibe M, Chandra S, Majumder S, Petersen GM, Rabe KG. Risk of Syndrome-Associated Cancers Among First-Degree Relatives of Patients With Pancreatic Ductal Adenocarcinoma With Pathogenic or Likely Pathogenic Germline Variants. JAMA Oncol 2023:2805076. [PMID: 37200008 PMCID: PMC10196930 DOI: 10.1001/jamaoncol.2023.0806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Importance Increased cancer risk in first-degree relatives of probands with pancreatic ductal adenocarcinoma (PDAC probands) who carry pathogenic or likely pathogenic germline variants (PGVs) in cancer syndrome-associated genes encourages cascade genetic testing. To date, unbiased risk estimates for the development of cancers on a gene-specific basis have not been assessed. Objective To quantify the risk of development of PDAC and extra-PDAC among first-degree relatives of PDAC probands who carry a PGV in 1 of 9 cancer syndrome-associated genes-ATM, BRCA1, BRCA2, PALB2, MLH1, MSH2, MSH6, PMS2, and CDKN2A. Design, Setting, and Participants This case series focused on first-degree relatives of PDAC probands carrying PGVs in specific cancer syndrome-associated genes. The cohort comprised clinic-ascertained patients enrolled in the Mayo Clinic Biospecimen Resource for Pancreas Research registry with germline genetic testing. In total, 234 PDAC probands carrying PGVs were drawn from the prospective research registry of 4562 participants who had undergone genetic testing of cancer syndrome-associated genes. Demographic and cancer-related family histories were obtained by questionnaire. The data were collected from October 1, 2000, to December 31, 2021. Main Outcomes and Measures For the PDAC probands, the genetic test results of the presence of PGVs in 9 cancer syndrome-associated genes were obtained by clinical testing. Cancers (ovary, breast, uterus or endometrial, colon, malignant melanoma, and pancreas) among first-degree relatives were reported by the probands. Standardized incidence ratios (SIRs) were used to estimate cancer risks among first-degree relatives of PDAC probands carrying a PGV. Results In total, 1670 first-degree relatives (mean [SD] age, 58.1 [17.8] years; 853 male [51.1%]) of 234 PDAC probands (mean [SD] age, 62.5 [10.1] years; 124 male [53.0%]; 219 [94.4%] White; 225 [98.7%] non-Hispanic or non-Latino]) were included in the study. There was a significantly increased risk of ovarian cancer in female first-degree relatives of probands who had variants in BRCA1 (SIR, 9.49; 95% CI, 3.06-22.14) and BRCA2 (SIR, 3.72; 95% CI, 1.36-8.11). Breast cancer risks were higher with BRCA2 variants (SIR, 2.62; 95% CI, 1.89-3.54). The risks of uterine or endometrial cancer (SIR, 6.53; 95% CI, 2.81-12.86) and colon cancer (SIR, 5.83; 95% CI, 3.70-8.75) were increased in first-degree relatives of probands who carried Lynch syndrome mismatch repair variants. Risk of PDAC was also increased for variants in ATM (SIR, 4.53; 95% CI, 2.69-7.16), BRCA2 (SIR, 3.45; 95% CI, 1.72-6.17), CDKN2A (SIR, 7.38; 95% CI, 3.18-14.54), and PALB2 (SIR, 5.39; 95% CI, 1.45-13.79). Melanoma risk was elevated for first-degree relatives of probands with CDKN2A variants (SIR, 7.47; 95% CI, 3.97-12.77). Conclusions and Relevance In this case series, the presence of PGVs in 9 cancer syndrome-associated genes in PDAC probands was found to be associated with increased risk of 6 types of cancers in first-degree relatives. These gene-specific PDAC and extra-PDAC cancer risks may provide justification for clinicians to counsel first-degree relatives about the relevance and importance of genetic cascade testing, with the goal of higher uptake of testing.
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Affiliation(s)
- Xuan Chen
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota
| | - Margaret A Meyer
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis
| | | | - Masayasu Horibe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shruti Chandra
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Shounak Majumder
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Gloria M Petersen
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Kari G Rabe
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
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Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med 2023; 25:100359. [PMID: 36745126 DOI: 10.1016/j.gim.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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5
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Schalk A, Cousin MA, Dsouza NR, Challman TD, Wain KE, Powis Z, Minks K, Trimouille A, Lasseaux E, Lacombe D, Angelini C, Michaud V, Van-Gils J, Spataro N, Ruiz A, Gabau E, Stolerman E, Washington C, Louie RJ, Lanpher BC, Kemppainen JL, Innes AM, Kooy RF, Meuwissen M, Goldenberg A, Lecoquierre F, Vera G, Diderich KEM, Sheidley BR, Achkar CME, Park M, Hamdan FF, Michaud JL, Lewis AJ, Zweier C, Reis A, Wagner M, Weigand H, Journel H, Keren B, Passemard S, Mignot C, van Gassen KL, Brilstra EH, Itzikowitz G, O’Heir E, Allen J, Donald KA, Korf BR, Skelton T, Thompson ML, Robin NH, Rudy N, Dobyns WB, Foss K, Zarate YA, Bosanko KA, Alembik Y, Durand B, Mau-Them FT, Ranza E, Blanc X, Antonarakis SE, McWalter K, Torti E, Millan F, Dameron A, Tokita MJ, Zimmermann MT, Klee EW, Piton A, Gerard B. De novo coding variants in the AGO1 gene cause a neurodevelopmental disorder with intellectual disability. J Med Genet 2022; 59:965-975. [PMID: 34930816 PMCID: PMC9241146 DOI: 10.1136/jmedgenet-2021-107751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/09/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND High-impact pathogenic variants in more than a thousand genes are involved in Mendelian forms of neurodevelopmental disorders (NDD). METHODS This study describes the molecular and clinical characterisation of 28 probands with NDD harbouring heterozygous AGO1 coding variants, occurring de novo for all those whose transmission could have been verified (26/28). RESULTS A total of 15 unique variants leading to amino acid changes or deletions were identified: 12 missense variants, two in-frame deletions of one codon, and one canonical splice variant leading to a deletion of two amino acid residues. Recurrently identified variants were present in several unrelated individuals: p.(Phe180del), p.(Leu190Pro), p.(Leu190Arg), p.(Gly199Ser), p.(Val254Ile) and p.(Glu376del). AGO1 encodes the Argonaute 1 protein, which functions in gene-silencing pathways mediated by small non-coding RNAs. Three-dimensional protein structure predictions suggest that these variants might alter the flexibility of the AGO1 linker domains, which likely would impair its function in mRNA processing. Affected individuals present with intellectual disability of varying severity, as well as speech and motor delay, autistic behaviour and additional behavioural manifestations. CONCLUSION Our study establishes that de novo coding variants in AGO1 are involved in a novel monogenic form of NDD, highly similar to the recently reported AGO2-related NDD.
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Affiliation(s)
- Audrey Schalk
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Margot A. Cousin
- Department of Health Sciences Research, Mayo Clinic,
Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
| | - Nikita R. Dsouza
- Bioinformatics Research and Development Laboratory,
Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
| | - Thomas D. Challman
- Autism & Developmental Medicine Institute, Geisinger,
Lewisburg, Pennsylvania, PA 17837, United States
| | - Karen E. Wain
- Autism & Developmental Medicine Institute, Geisinger,
Lewisburg, Pennsylvania, PA 17837, United States
| | - Zöe Powis
- Department of Clinical Genomics, Ambry Genetics, Aliso
Viejo, California, CA 92656, United States
| | - Kelly Minks
- Department of Clinical Genomics, Ambry Genetics, Aliso
Viejo, California, CA 92656, United States
| | - Aurélien Trimouille
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Eulalie Lasseaux
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
| | - Didier Lacombe
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Chloé Angelini
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Vincent Michaud
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
- Maladies rares: Génétique et
Métabolisme (MRGM), INSERM U1211, Université de Bordeaux,
Bordeaux
| | - Julien Van-Gils
- Service de Génétique Médicale, Centre
de Référence Anomalies du Développement et Syndrome
Malformatifs, CHU de Bordeaux, Bordeaux, France
| | - Nino Spataro
- Genetics Laboratory, UDIAT-Centre Diagnòstic. Parc
Taulí Hospital Universitari. Institut d’Investigació i
Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona.
Sabadell, Spain
| | - Anna Ruiz
- Genetics Laboratory, UDIAT-Centre Diagnòstic. Parc
Taulí Hospital Universitari. Institut d’Investigació i
Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona.
Sabadell, Spain
| | - Elizabeth Gabau
- Paediatric Unit. ParcTaulí Hospital Universitari.
Institut d’Investigació i Innovació Parc Taulí I3PT.
Universitat Autònoma de Barcelona. Sabadell, Spain
| | - Elliot Stolerman
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Camerun Washington
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Raymond J. Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester,
Minnesota, MN 55905, United States
| | - Jennifer L. Kemppainen
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Department of Clinical Genomics, Mayo Clinic, Rochester,
Minnesota, MN 55905, United States
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta
Children’s Hospital Research Institute, Cumming School of Medicine,
University of Calgary, Calgary, AB, Canada
| | - R. Frank Kooy
- Department of Medical Genetics, University and University
Hospital Antwerp, Antwerp, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University and University
Hospital Antwerp, Antwerp, Belgium
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - Gabriella Vera
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen
University Hospital, Department of Genetics and Reference Center for Developmental
Disorders, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen,
France
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center,
Rotterdam, The Netherlands
| | - Beth Rosen Sheidley
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Christelle Moufawad El Achkar
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Meredith Park
- Division of Epilepsy and Clinical Neurophysiology,
Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts,
MA 02115, United States
| | - Fadi F. Hamdan
- Division of Medical Genetics, Department of Pediatrics,
CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Jacques L. Michaud
- Division of Medical Genetics, Department of Pediatrics,
CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Ann J. Lewis
- Pediatric Neurology, Kaiser Permanente Santa Clara
Homestead, Santa Clara, United States
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern
University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics,
Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - André Reis
- Department of Human Genetics, Inselspital, Bern
University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics,
Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen,
Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich,
Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum
München, Neuherberg, Germany
| | - Heike Weigand
- Department of Pediatric Neurology, Developmental Medicine
and Social Pediatrics, Dr. von Hauner’s Children’s Hospital,
University of Munich, Munich, Germany
| | - Hubert Journel
- Service de Génétique Médicale,
Hôpital Chubert, Vannes, France
| | - Boris Keren
- Département de Génétique et de
Cytogénétique, Centre de Reference Déficience Intellectuelle de
Causes Rares, GRC UPMC « Déficience Intellectuelle et Autisme
», Hôpital Pitié-Salpêtrière, AP-HP, Paris,
France
- INSERM U 1127, CNRS UMR 7225, Sorbonne
Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la
Moelle épinière, ICM, Paris, France
| | | | - Cyril Mignot
- Département de Génétique et de
Cytogénétique, Centre de Reference Déficience Intellectuelle de
Causes Rares, GRC UPMC « Déficience Intellectuelle et Autisme
», Hôpital Pitié-Salpêtrière, AP-HP, Paris,
France
- INSERM U 1127, CNRS UMR 7225, Sorbonne
Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la
Moelle épinière, ICM, Paris, France
| | | | - Eva H. Brilstra
- Department of Genetics, Center for Molecular Medicine,
University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gina Itzikowitz
- Department of Paediatrics and Child Health, Red Cross War
Memorial Children’s Hospital, University of Cape Town, SA
| | - Emily O’Heir
- Center for Mendelian Genomics and Program in Medical and
Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston
Children’s Hospital, Boston, MA, USA
| | - Jake Allen
- Stanley Center for Psychiatric Research, Broad Institute
of MIT and Harvard, Cambridge, MA, USA
| | - Kirsten A. Donald
- Department of Paediatrics and Child Health, Red Cross War
Memorial Children’s Hospital, University of Cape Town, SA
- Neuroscience Institute, University of Cape Town, SA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at
Birmingham, Birmingham, AL 35294, USA
| | - Tammi Skelton
- Department of Genetics, University of Alabama at
Birmingham, Birmingham, AL 35294, USA
| | - Michelle L Thompson
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
- HudsonAlpha Institute for Biotechnology, Huntsville,
Alabama, USA
| | - Nathaniel H. Robin
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Natasha Rudy
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - William B. Dobyns
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Kimberly Foss
- Department of Pediatrics (Genetics) and Neurology,
University of Washington, and Seattle Children’s Research Institute, Seattle,
Washington, USA
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of
Arkansas for Medical Sciences, Little Rock, USA
| | - Katherine A. Bosanko
- Section of Genetics and Metabolism, University of
Arkansas for Medical Sciences, Little Rock, USA
| | - Yves Alembik
- Service de Génétique Médicale,
Institut de génétique médicale d’Alsace (IGMA),
Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Benjamin Durand
- Service de Génétique Médicale,
Institut de génétique médicale d’Alsace (IGMA),
Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Frédéric Tran Mau-Them
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, 1207
Geneva, Switzerland
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, 1207
Geneva, Switzerland
| | | | | | | | | | | | | | - Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory,
Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
- Clinical and Translational Sciences Institute, Medical
College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
| | - Eric W. Klee
- Department of Health Sciences Research, Mayo Clinic,
Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester,
MN, 55905, United States
- Greenwood Genetic Center, 106 Gregor Mendel Cir,
Greenwood, SC 29646, USA
| | - Amélie Piton
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
- Institut de Genetique et de Biologie Moleculaire et
Cellulaire, Illkirch 67400, France
| | - Bénédicte Gerard
- Laboratoire de Diagnostic Génétique, Institut
de génétique médicale d’Alsace (IGMA), Hôpitaux
Universitaires de Strasbourg, Strasbourg, France
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6
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Rabe KG, Stevens MA, Hernández AT, Chandra S, Hubbard JM, Kemppainen JL, Majumder S, Petersen GM. Pancreatic cancer risk to siblings of probands in bilineal cancer settings. Genet Med 2022; 24:1008-1016. [PMID: 35227607 PMCID: PMC9326771 DOI: 10.1016/j.gim.2022.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Pancreatic cancer (PC) risk is increased in families, but PC risk and risk perception have been understudied when both parents have cancer. METHODS An unbiased method defining cancer triads (proband with PC and both parents with cancer) in a prospective registry estimated risk of PC to probands' siblings in triad group 1 (no parent with PC), group 2 (1 parent with PC), and group 3 (both parents with PC). We estimated standardized incidence ratios (SIRs) using a Surveillance, Epidemiology, and End Results (SEER) reference. We also estimated the risk when triad probands carried germline pathogenic/likely pathogenic variants in any of the 6 PC-associated genes (ATM, BRCA1, BRCA2, CDKN2A, MLH1, and TP53). PC risk perception/concern was surveyed in siblings and controls. RESULTS Risk of PC was higher (SIR = 3.5; 95% CI = 2.2-5.2) in 933 at-risk siblings from 297 triads. Risk increased by triad group: 2.8 (95% CI = 1.5-4.5); 4.5 (95% CI = 1.6-9.7); and 21.2 (95% CI = 4.3-62.0). SIR in variant-negative triads was 3.0 (95% CI = 1.6-5.0), whereas SIR in variant-positive triads was 10.0 (95% CI = 3.2-23.4). Siblings' perceived risk/concern of developing PC increased by triad group. CONCLUSION Sibling risks were 2.8- to 21.2-fold higher than that of the general population. Positive variant status increased the risk in triads. Increasing number of PC cases in a triad was associated with increased concern and perceived PC risk.
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Affiliation(s)
- Kari G Rabe
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Maria A Stevens
- Division of Health Care Policy and Research, Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN
| | - Amanda Toledo Hernández
- School of Medicine, Medical Science Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Shruti Chandra
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | | | | | - Shounak Majumder
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Gloria M Petersen
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN.
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7
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Pinto E Vairo F, Prochnow C, Kemppainen JL, Lisi EC, Steyermark JM, Kruisselbrink TM, Pichurin PN, Dhamija R, Hager MM, Albadri S, Cornell LD, Lazaridis KN, Klee EW, Senum SR, El Ters M, Amer H, Baudhuin LM, Moyer AM, Keddis MT, Zand L, Sas DJ, Erickson SB, Fervenza FC, Lieske JC, Harris PC, Hogan MC. Genomics Integration Into Nephrology Practice. Kidney Med 2021; 3:785-798. [PMID: 34746741 PMCID: PMC8551494 DOI: 10.1016/j.xkme.2021.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
RATIONALE & OBJECTIVE The etiology of kidney disease remains unknown in many individuals with chronic kidney disease (CKD). We created the Mayo Clinic Nephrology Genomics Clinic to improve our ability to integrate genomic and clinical data to identify the etiology of unexplained CKD. STUDY DESIGN Retrospective study. SETTING & PARTICIPANTS An essential component of our program is the Nephrology Genomics Board which consists of nephrologists, geneticists, pathologists, translational omics scientists, and trainees who interpret the patient's clinical and genetic data. Since September 2016, the Board has reviewed 163 cases (15 cystic, 100 glomerular, 6 congenital anomalies of kidney and urinary tract (CAKUT), 20 stones, 15 tubulointerstitial, and 13 other). ANALYTICAL APPROACH Testing was performed with targeted panels, single gene analysis, or analysis of kidney-related genes from exome sequencing. Variant classification was obtained based on the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines. RESULTS A definitive genetic diagnosis was achieved for 50 families (30.7%). The highest diagnostic yield was obtained in individuals with tubulointerstitial diseases (53.3%), followed by congenital anomalies of the kidney and urological tract (33.3%), glomerular (31%), cysts (26.7%), stones (25%), and others (15.4%). A further 20 (12.3%) patients had variants of interest, and variant segregation, and research activities (exome, genome, or transcriptome sequencing) are ongoing for 44 (40%) unresolved families. LIMITATIONS Possible overestimation of diagnostic rate due to inclusion of individuals with variants with evidence of pathogenicity but classified as of uncertain significance by the clinical laboratory. CONCLUSIONS Integration of genomic and research testing and multidisciplinary evaluation in a nephrology cohort with CKD of unknown etiology or suspected monogenic disease provided a diagnosis in a third of families. These diagnoses had prognostic implications, and often changes in management were implemented.
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Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Carri Prochnow
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | | | - Emily C Lisi
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Joan M Steyermark
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Rhadika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, Arizona
| | - Megan M Hager
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, Arizona
| | - Sam Albadri
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lynn D Cornell
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Sarah R Senum
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Mireille El Ters
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Hatem Amer
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Linnea M Baudhuin
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ann M Moyer
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mira T Keddis
- Division of Nephrology, Mayo Clinic, Scottsdale, Arizona
| | - Ladan Zand
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - David J Sas
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Stephen B Erickson
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | | | - John C Lieske
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Peter C Harris
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Marie C Hogan
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
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8
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Pinto E Vairo F, Kemppainen JL, Lieske JC, Harris PC, Hogan MC. Establishing a nephrology genetic clinic. Kidney Int 2021; 100:254-259. [PMID: 34294204 DOI: 10.1016/j.kint.2021.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA.
| | | | - John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Marie C Hogan
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA.
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9
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Pinto E Vairo F, Koster MJ, Kemppainen JL, Thomas BC, Warrington KJ. Comment on: Anti-tumour necrosis factor treatment for the prevention of ischaemic events in patients with deficiency of adenosine deaminase 2 (DADA2). Rheumatology (Oxford) 2021; 60:e218-e219. [PMID: 33515254 DOI: 10.1093/rheumatology/keab081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Filippo Pinto E Vairo
- Department of Clinical Genomics, Center for Individualized Medicine, Rochester, MN, USA
| | - Matthew J Koster
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jennifer L Kemppainen
- Department of Clinical Genomics, Center for Individualized Medicine, Rochester, MN, USA
| | - Brittany C Thomas
- Department of Clinical Genomics, Center for Individualized Medicine, Rochester, MN, USA
| | - Kenneth J Warrington
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
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10
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Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med 2021; 23:498-507. [PMID: 33144682 DOI: 10.1038/s41436-020-01005-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Exome sequencing often identifies pathogenic genetic variants in patients with undiagnosed diseases. Nevertheless, frequent findings of variants of uncertain significance necessitate additional efforts to establish causality before reaching a conclusive diagnosis. To provide comprehensive genomic testing to patients with undiagnosed disease, we established an Individualized Medicine Clinic, which offered clinical exome testing and included a Translational Omics Program (TOP) that provided variant curation, research activities, or research exome sequencing. METHODS From 2012 to 2018, 1101 unselected patients with undiagnosed diseases received exome testing. Outcomes were reviewed to assess impact of the TOP and patient characteristics on diagnostic rates through descriptive and multivariate analyses. RESULTS The overall diagnostic yield was 24.9% (274 of 1101 patients), with 174 (15.8% of 1101) diagnosed on the basis of clinical exome sequencing alone. Four hundred twenty-three patients with nondiagnostic or without access to clinical exome sequencing were evaluated by the TOP, with 100 (9% of 1101) patients receiving a diagnosis, accounting for 36.5% of the diagnostic yield. The identification of a genetic diagnosis was influenced by the age at time of testing and the disease phenotype of the patient. CONCLUSION Integration of translational research activities into clinical practice of a tertiary medical center can significantly increase the diagnostic yield of patients with undiagnosed disease.
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Affiliation(s)
- Eric W Klee
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
| | - Margot A Cousin
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Joel A Morales-Rosado
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - W Garrett Jenkinson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ashley N Sigafoos
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya L Schwab
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul A Urrutia
- Division of Research, Department of Surgery and the Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Aditi Gupta
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole J Boczek
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carri A Prochnow
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rebecca J Lowy
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tammy M McAllister
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Stacy L Aoudia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Teresa M Kruisselbrink
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jennifer L Kemppainen
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Laura J Fisher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Megan M Hager
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Sarah A Kroc
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Bertsch
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Katherine E Agre
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Laura M Rust
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Scott A Beck
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Marissa S Ellingson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kristen J Rasmussen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carrie A Lahner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Zhiyv Niu
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Ferber
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Karl J Clark
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava-Kozicz
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H Gavrilova
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA.,Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Gianrico Farrugia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Konstantinos N Lazaridis
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA.
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11
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Qureshi MY, Patterson MC, Clark V, Johnson JN, Moutvic MA, Driscoll SW, Kemppainen JL, Huston J, Anderson JR, Badley AD, Tebben PJ, Wackel P, Oglesbee D, Glockner J, Schreiner G, Dugar S, Touchette JC, Gavrilova RH. Safety and efficacy of (+)-epicatechin in subjects with Friedreich's ataxia: A phase II, open-label, prospective study. J Inherit Metab Dis 2021; 44:502-514. [PMID: 32677106 DOI: 10.1002/jimd.12285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/23/2020] [Accepted: 07/13/2020] [Indexed: 02/02/2023]
Abstract
BACKGROUND (+)-Epicatechin (EPI) induces mitochondrial biogenesis and antioxidant metabolism in muscle fibers and neurons. We aimed to evaluate safety and efficacy of (+)-EPI in pediatric subjects with Friedreich's ataxia (FRDA). METHODS This was a phase II, open-label, baseline-controlled single-center trial including 10 participants ages 10 to 22 with confirmed FA diagnosis. (+)-EPI was administered orally at 75 mg/d for 24 weeks, with escalation to 150 mg/d at 12 weeks for subjects not showing improvement of neuromuscular, neurological or cardiac endpoints. Neurological endpoints were change from baseline in Friedreich's Ataxia Rating Scale (FARS) and 8-m timed walk. Cardiac endpoints were changes from baseline in left ventricular (LV) structure and function by cardiac magnetic resonance imaging (MRI) and echocardiogram, changes in cardiac electrophysiology, and changes in biomarkers for heart failure and hypertrophy. RESULTS Mean FARS/modified (m)FARS scores showed nonstatistically significant improvement by both group and individual analysis. FARS/mFARS scores improved in 5/9 subjects (56%), 8-m walk in 3/9 (33%), 9-peg hole test in 6/10 (60%). LV mass index by cardiac MRI was significantly reduced at 12 weeks (P = .045), and was improved in 7/10 (70%) subjects at 24 weeks. Mean LV ejection fraction was increased at 24 weeks (P = .008) compared to baseline. Mean maximal septal thickness by echocardiography was increased at 24 weeks (P = .031). There were no serious adverse events. CONCLUSION (+)-EPI was well tolerated over 24 weeks at up to 150 mg/d. Improvement was observed in cardiac structure and function in subset of subjects with FRDA without statistically significant improvement in primary neurological outcomes. SYNOPSIS A (+)-epicatechin showed improvement of cardiac function, nonsignificant reduction of FARS/mFARS scores, and sustained significant upregulation of muscle-regeneration biomarker follistatin.
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Affiliation(s)
- Muhammad Yasir Qureshi
- Department of Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
- Division of Pediatric Cardiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Marc C Patterson
- Department of Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Vicki Clark
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jonathan N Johnson
- Department of Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
- Division of Pediatric Cardiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Margaret A Moutvic
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, Minnesota, USA
| | - Sherilyn W Driscoll
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, Minnesota, USA
| | | | - John Huston
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jeff R Anderson
- Office of Translation to Practice, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew D Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter J Tebben
- Division of Endocrinology, Mayo Clinic, Rochester, Minnesota, USA
| | - Philip Wackel
- Department of Pediatrics, Mayo Clinic, Rochester, Minnesota, USA
- Division of Pediatric Cardiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Devin Oglesbee
- Department of Pathology and Laboratory Medicine, Rochester, Minnesota, USA
| | - James Glockner
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | - Ralitza H Gavrilova
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
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12
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Macke EL, Pinto E Vairo F, Manian DV, Smith AR, Kemppainen JL, Klee EW, Stephens MC, Joshi AY. Successful Treatment of Skewed Lyonization Associated with X-Linked CGD in a Female Presenting with Recalcitrant Crohn's Disease. J Clin Immunol 2020; 40:1056-1061. [PMID: 32720229 DOI: 10.1007/s10875-020-00822-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/02/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Erica L Macke
- Center for Individualized Medicine, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA.,Department of Clinical Genomics, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA
| | | | - Angela R Smith
- Department of Pediatrics, Division of Pediatric Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Jennifer L Kemppainen
- Department of Clinical Genomics, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA.,Department of Clinical Genomics, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA.,Department of Health Sciences Research, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA
| | - Michael C Stephens
- Center for Individualized Medicine, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA.,Department of Pediatric Gastroenterology, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA
| | - Avni Y Joshi
- Division of Pediatric Allergy and Immunology, Mayo Clinic Childrens Center, 200 First St SW, Rochester, MN, 55905, USA. .,Department of Pediatric and Adolescent Medicine, Mayo Clinic Childrens Center, Rochester, MN, 55905, USA.
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13
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Ferrer A, Schultz-Rogers L, Kaiwar C, Kemppainen JL, Klee EW, Gavrilova RH. Three rare disease diagnoses in one patient through exome sequencing. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004390. [PMID: 31427378 PMCID: PMC6913146 DOI: 10.1101/mcs.a004390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/14/2019] [Indexed: 01/01/2023] Open
Abstract
Diagnostic exome sequencing yields a single genetic diagnosis in ∼30% of cases, and according to recent studies the prevalence of identifying two genetic conditions in a single individual range between 4.6% and 7%. We present a patient diagnosed with three different rare conditions, each explained by a pathogenic variant in a different gene. A 17-yr-old female was evaluated for a history of motor and speech delay, scoliosis, distinctive craniofacial features, and dry skin in the Department of Clinical Genomics at Mayo Clinic. Her distinctive features included prominent forehead, epicanthus, depressed nasal bridge, narrow mouth, prognathism, malar flattening, and oligodontia. Family history was notable for dry skin in her mother and missing teeth in the paternal grandmother. Previous diagnostic testing was unrevealing including biochemical testing, echocardiogram, abdominal ultrasound, and electroencephalogram. Previous genetic testing included a microarray-based comparative genomic hybridization that was reported normal. Three pathogenic loss-of-function heterozygous variants were identified by exome trio sequencing, each linked to different genetic conditions: SIN3A (Witteveen–Kolk syndrome), FLG (dermatitis), and EDAR (ectodermal dysplasia). Together, these three genetic alterations could explain the patient's overall phenotype. This patient demonstrates the importance of performing a thorough curation of exome data when presented with a complex phenotype. Although phenotypic variability can explain some of these situations, the hypothesis of multiple diseases coexisting in a single patient should never be disregarded completely.
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Affiliation(s)
- Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Laura Schultz-Rogers
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Charu Kaiwar
- Invitae Corporation, San Francisco, California 94103, USA
| | | | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Ralitza H Gavrilova
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Neurology, Mayo Clinic, Rochester, Minnesota 55905, USA
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14
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Abstract
Case series Patients: 38, female • 28, female • 41, female • 18, female • 23, male Final Diagnosis: Woodhouse-Sakati syndrome Symptoms: Hypogonadism • dystonia • alopecia • hearing loss • diabetes Medication: — Clinical Procedure: — Specialty: Endocrinology and Metabolic
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Affiliation(s)
- Mohammad Almeqdadi
- Department of Internal Medicine, St. Elizabeth's Medical Center, Boston, MA, USA
| | | | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H Gavrilova
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Neurology, Mayo Clinic, Rochester, MN, USA
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15
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Blackburn PR, Tischer A, Zimmermann MT, Kemppainen JL, Sastry S, Knight Johnson AE, Cousin MA, Boczek NJ, Oliver G, Misra VK, Gavrilova RH, Lomberk G, Auton M, Urrutia R, Klee EW. A Novel Kleefstra Syndrome-associated Variant That Affects the Conserved TPL X Motif within the Ankyrin Repeat of EHMT1 Leads to Abnormal Protein Folding. J Biol Chem 2017; 292:3866-3876. [PMID: 28057753 PMCID: PMC5339767 DOI: 10.1074/jbc.m116.770545] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/05/2017] [Indexed: 12/26/2022] Open
Abstract
Kleefstra syndrome (KS) (Mendelian Inheritance in Man (MIM) no. 610253), also known as 9q34 deletion syndrome, is an autosomal dominant disorder caused by haploinsufficiency of euchromatic histone methyltransferase-1 (EHMT1). The clinical phenotype of KS includes moderate to severe intellectual disability with absent speech, hypotonia, brachycephaly, congenital heart defects, and dysmorphic facial features with hypertelorism, synophrys, macroglossia, protruding tongue, and prognathism. Only a few cases of de novo missense mutations in EHMT1 giving rise to KS have been described. However, some EHMT1 variants have been described in individuals presenting with autism spectrum disorder or mild intellectual disability, suggesting that the phenotypic spectrum resulting from EHMT1 alterations may be quite broad. In this report, we describe two unrelated patients with complex medical histories consistent with KS in whom next generation sequencing identified the same novel c.2426C>T (p.P809L) missense variant in EHMT1. To examine the functional significance of this novel variant, we performed molecular dynamics simulations of the wild type and p.P809L variant, which predicted that the latter would have a propensity to misfold, leading to abnormal histone mark binding. Recombinant EHMT1 p.P809L was also studied using far UV circular dichroism spectroscopy and intrinsic protein fluorescence. These functional studies confirmed the model-based hypotheses and provided evidence for protein misfolding and aberrant target recognition as the underlying pathogenic mechanism for this novel KS-associated variant. This is the first report to suggest that missense variants in EHMT1 that lead to protein misfolding and disrupted histone mark binding can lead to KS.
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Affiliation(s)
- Patrick R Blackburn
- From the Center for Individualized Medicine and.,the Department of Health Science Research, Mayo Clinic, Jacksonville, Florida 32224
| | - Alexander Tischer
- the Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology
| | - Michael T Zimmermann
- the Department of Health Science Research, Division of Biomedical Statistics and Informatics
| | | | - Sujatha Sastry
- the Department of Pediatrics, Division of Genetics and Metabolic Disorders, Wayne State University School of Medicine, Detroit, Michigan 48201, and
| | - Amy E Knight Johnson
- the Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
| | - Margot A Cousin
- the Center for Individualized Medicine.,the Department of Health Science Research
| | - Nicole J Boczek
- the Center for Individualized Medicine.,the Department of Health Science Research
| | | | - Vinod K Misra
- the Department of Pediatrics, Division of Genetics and Metabolic Disorders, Wayne State University School of Medicine, Detroit, Michigan 48201, and
| | | | - Gwen Lomberk
- the Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Matthew Auton
- the Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology
| | - Raul Urrutia
- the Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905,
| | - Eric W Klee
- the Department of Clinical Genomics, .,the Center for Individualized Medicine.,the Department of Health Science Research
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