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Marhabaie M, Hickey SE, Miller K, Grischow O, Schieffer KM, Franklin SJ, Gordon DM, Choi S, Mihalic Mosher T, White P, Koboldt DC, Wilson RK. Maternal mosaicism for a missense variant in the SMS gene that causes Snyder-Robinson syndrome. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006122. [PMID: 34667072 PMCID: PMC8751409 DOI: 10.1101/mcs.a006122] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/30/2021] [Indexed: 11/25/2022] Open
Abstract
There is increasing recognition for the contribution of genetic mosaicism to human disease, particularly as high-throughput sequencing has enabled detection of sequence variants at very low allele frequencies. Here, we describe an infant male who presented at 9 mo of age with hypotonia, dysmorphic features, congenital heart disease, hyperinsulinemic hypoglycemia, hypothyroidism, and bilateral sensorineural hearing loss. Whole-genome sequencing of the proband and the parents uncovered an apparent de novo mutation in the X-linked SMS gene. SMS encodes spermine synthase, which catalyzes the production of spermine from spermidine. Inactivation of the SMS gene disrupts the spermidine/spermine ratio, resulting in Snyder–Robinson syndrome. The variant in our patient is absent from the gnomAD and ExAC databases and causes a missense change (p.Arg130Cys) predicted to be damaging by most in silico tools. Although Sanger sequencing confirmed the de novo status in our proband, polymerase chain reaction (PCR) and deep targeted resequencing to ∼84,000×–175,000× depth revealed that the variant is present in blood from the unaffected mother at ∼3% variant allele frequency. Our findings thus provided a long-sought diagnosis for the family while highlighting the role of parental mosaicism in severe genetic disorders.
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Affiliation(s)
- Mohammad Marhabaie
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Scott E Hickey
- Division of Genetic and Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics at The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
| | - Katherine Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Olivia Grischow
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Samuel J Franklin
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - David M Gordon
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Samantha Choi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Theresa Mihalic Mosher
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics at The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics at The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics at The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
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Miller CR, Lee K, Pfau RB, Reshmi SC, Corsmeier DJ, Hashimoto S, Dave-Wala A, Jayaraman V, Koboldt D, Matthews T, Mouhlas D, Stein M, McKinney A, Grossman T, Kelly BJ, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE. Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005231. [PMID: 32371413 PMCID: PMC7304353 DOI: 10.1101/mcs.a005231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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] [Received: 02/15/2020] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Exome sequencing (ES) has become an important tool in pediatric genomic medicine, improving identification of disease-associated variation due to assay breadth. Depth is also afforded by ES, enabling detection of lower-frequency mosaic variation compared to Sanger sequencing in the studied tissue, thus enhancing diagnostic yield. Within a pediatric tertiary-care hospital, we report two years of clinical ES data from probands evaluated for genetic disease to assess diagnostic yield, characteristics of causal variants, and prevalence of mosaicism among disease-causing variants. Exome-derived, phenotype-driven variant data from 357 probands was analyzed concurrent with parental ES data, when available. Blood was the source of nucleic acid. Sequence read alignments were manually reviewed for all assessed variants. Sanger sequencing was used for suspected de novo or mosaic variation. Clinical provider notes were reviewed to determine concordance between laboratory-reported data and the ordering provider's interpretation of variant-associated disease causality. Laboratory-derived diagnostic yield and provider-substantiated diagnoses had 91.4% concordance. The cohort returned 117 provider-substantiated diagnoses among 115 probands for a diagnostic yield of 32.2%. De novo variants represented 64.9% of disease-associated variation within trio analyses. Among the 115 probands, five harbored disease-associated somatic mosaic variation. Two additional probands were observed to inherit a disease-associated variant from an unaffected mosaic parent. Among inheritance patterns, de novo variation was the most frequent disease etiology. Somatic mosaicism is increasingly recognized as a significant contributor to genetic disease, particularly with increased sequence depth attainable from ES. This report highlights the potential and importance of detecting mosaicism in ES.
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Affiliation(s)
- Cecelia R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Ruthann B Pfau
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shalini C Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Donald J Corsmeier
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Sayaka Hashimoto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Ashita Dave-Wala
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Daniel Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Theodora Matthews
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Danielle Mouhlas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Maggie Stein
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Tom Grossman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
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Koboldt DC, Kastury RD, Waldrop MA, Kelly BJ, Mosher TM, McLaughlin H, Corsmeier D, Slaughter JL, Flanigan KM, McBride KL, Mehta L, Wilson RK, White P. In-frame de novo mutation in BICD2 in two patients with muscular atrophy and arthrogryposis. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003160. [PMID: 30054298 PMCID: PMC6169820 DOI: 10.1101/mcs.a003160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 05/10/2018] [Accepted: 07/23/2018] [Indexed: 01/10/2023] Open
Abstract
We describe two unrelated patients, a 12-yr-old female and a 6-yr-old male, with congenital contractures and severe congenital muscular atrophy. Exome and genome sequencing of the probands and their unaffected parents revealed that they have the same de novo deletion in BICD2 (c.1636_1638delAAT). The variant, which has never been reported, results in an in-frame 3-bp deletion and is predicted to cause loss of an evolutionarily conserved asparagine residue at position 546 in the protein. Missense mutations in BICD2 cause autosomal dominant spinal muscular atrophy, lower-extremity predominant 2 (SMALED2), a disease characterized by muscle weakness and arthrogryposis of early onset and slow progression. The p.Asn546del clusters with four pathogenic missense variants in a region that likely binds molecular motor KIF5A. Protein modeling suggests that removing the highly conserved asparagine residue alters BICD2 protein structure. Our findings support a broader phenotypic spectrum of BICD2 mutations that may include severe manifestations such as cerebral atrophy, seizures, dysmorphic facial features, and profound muscular atrophy.
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Affiliation(s)
- Daniel C Koboldt
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Rama D Kastury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Megan A Waldrop
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA.,Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Benjamin J Kelly
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Theresa Mihalic Mosher
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | | | - Don Corsmeier
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Jonathan L Slaughter
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA.,Center for Perinatal Research and Division of Neonatology, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Kevin M Flanigan
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA.,Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Neurology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kim L McBride
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Lakshmi Mehta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Peter White
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
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Koboldt DC, Mihalic Mosher T, Kelly BJ, Sites E, Bartholomew D, Hickey SE, McBride K, Wilson RK, White P. A de novo nonsense mutation in ASXL3 shared by siblings with Bainbridge-Ropers syndrome. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002410. [PMID: 29305346 PMCID: PMC5983172 DOI: 10.1101/mcs.a002410] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 10/26/2017] [Accepted: 12/26/2017] [Indexed: 12/31/2022] Open
Abstract
Two sisters (ages 16 yr and 15 yr) have been followed by our clinical genetics team for several years. Both girls have severe intellectual disability, hypotonia, seizures, and distinctive craniofacial features. The parents are healthy and have no other children. Oligo array, fragile X testing, and numerous single-gene tests were negative. All four family members underwent research exome sequencing, which revealed a heterozygous nonsense mutation in ASXL3 (p.R1036X) that segregated with disease. Exome data and independent Sanger sequencing confirmed that the variant is de novo, suggesting possible germline mosaicism in one parent. The p.R1036X variant has never been observed in healthy human populations and has been previously reported as a pathogenic mutation. Truncating de novo mutations in ASXL3 cause Bainbridge–Ropers syndrome (BRPS), a developmental disorder with similarities to Bohring–Opitz syndrome. Fewer than 30 BRPS patients have been described in the literature; to our knowledge, this is the first report of the disorder in two related individuals. Our findings lend further support to intellectual disability, absent speech, autistic traits, hypotonia, and distinctive facial appearance as common emerging features of Bainbridge–Ropers syndrome.
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Affiliation(s)
- Daniel C Koboldt
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA
| | - Theresa Mihalic Mosher
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Benjamin J Kelly
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Emily Sites
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Dennis Bartholomew
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Kim McBride
- Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA.,Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Center for Cardiovascular and Pulmonary Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Richard K Wilson
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA
| | - Peter White
- Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA
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Kaiwar C, Zimmermann MT, Ferber MJ, Niu Z, Urrutia RA, Klee EW, Babovic-Vuksanovic D. Novel NR2F1 variants likely disrupt DNA binding: molecular modeling in two cases, review of published cases, genotype-phenotype correlation, and phenotypic expansion of the Bosch-Boonstra-Schaaf optic atrophy syndrome. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a002162. [PMID: 28963436 PMCID: PMC5701304 DOI: 10.1101/mcs.a002162] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 05/24/2017] [Accepted: 08/28/2017] [Indexed: 01/08/2023] Open
Abstract
Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS) is a recently described autosomal dominant disorder caused by mutations in the NR2F1 gene. There are presently 28 cases of BBSOAS described in the literature. Its common features include developmental delay, intellectual disability, hypotonia, optic nerve atrophy, attention deficit disorder, autism spectrum disorder, seizures, hearing defects, spasticity, and thinning of the corpus callosum. Here we report two unrelated probands with novel, de novo, missense variants in NR2F1 The first is a 14-yr-old male patient with hypotonia, intellectual disability, optic nerve hypoplasia, delayed bone age, short stature, and altered neurotransmitter levels on cerebrospinal fluid testing. The second is a 5-yr-old female with severe developmental delay, motor and speech delay, and repetitive motion behavior. Whole-exome sequencing identified a novel missense NR2F1 variant in each case, Cys86Phe in the DNA-binding domain in Case 1, and a Leu372Pro in the ligand-binding domain in Case 2. The presence of clinical findings compatible with BBSOAS along with structural analysis at atomic resolution using homology-based molecular modeling and molecular dynamic simulations, support the pathogenicity of these variants for BBSOAS. Short stature, abnormal CNS neurotransmitters, and macrocephaly have not been previously reported for this syndrome and may represent a phenotypic expansion of BBSOAS. A review of published cases along with new evidence from this report support genotype-phenotype correlations for this disorder.
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Affiliation(s)
- Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona 85259, USA
| | - Michael T Zimmermann
- Department of Health Sciences Research, Mayo Clinic, Division of Biomedical Statistic and Informatics, Rochester, Minnesota 55905, USA
| | - Matthew J Ferber
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Zhiyv Niu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Raul A Urrutia
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Medicine, Gastroenterology Research Unit, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Department of Health Sciences Research, Mayo Clinic, Division of Biomedical Statistic and Informatics, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Dusica Babovic-Vuksanovic
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
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