المؤلفون: Rego, Shannon, Hoban, Hannah, Outram, Simon, Zamora, Astrid N, Chen, Flavia, Sahin-Hodoglugil, Nuriye, Anguiano, Beatriz, Norstad, Matthew, Yip, Tiffany, Lianoglou, Billie, Sparks, Teresa N, Norton, Mary E, Koenig, Barbara A, Slavotinek, Anne M, Ackerman, Sara L

المصدر: Genetics in Medicine. 24(6)

مصطلحات موضوعية: Biological Sciences, Genetics, Pediatric, Human Genome, Clinical Research, Child, Exome, Family, Female, Genome, Human, Genomics, Humans, Pregnancy, Exome Sequencing, Exome sequencing, Genome sequencing, Secondary findings, Clinical Sciences, Genetics & Heredity

الوصف: PurposePatients undergoing clinical exome sequencing (ES) are routinely offered the option to receive secondary findings (SF). However, little is known about the views of individuals from underrepresented minority pediatric or prenatal populations regarding SF.MethodsWe explored the preferences for receiving hypothetical categories of SF (H-SF) and reasons for accepting or declining actual SF through surveying (n = 149) and/or interviewing (n = 47) 190 families undergoing pediatric or prenatal ES.ResultsUnderrepresented minorities made up 75% of the probands. In total, 150 families (79%) accepted SF as part of their child/fetus's ES. Most families (63%) wanted all categories of H-SF. Those who declined SF as part of ES were less likely to want H-SF across all categories. Interview findings indicate that some families did not recall their SF decision. Preparing for the future was a major motivator for accepting SF, and concerns about privacy, discrimination, and psychological effect drove decliners.ConclusionA notable subset of families (37%) did not want at least 1 category of H-SF, suggesting more hesitancy about receiving all available results than previously reported. The lack of recollection of SF decisions suggests a need for alternative communication approaches. Results highlight the importance of the inclusion of diverse populations in genomic research.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/174592k3Test

المؤلفون: Swanson, Kate, Sparks, Teresa N, Lianoglou, Billie R, Chen, Flavia, Downum, Sarah, Patel, Sachi, Rego, Shannon, Yip, Tiffany, Van Ziffle, Jessica, Koenig, Barbara A, Slavotinek, Anne M, Norton, Mary E

المصدر: Prenatal Diagnosis. 42(6)

مصطلحات موضوعية: Reproductive Medicine, Biomedical and Clinical Sciences, Clinical Sciences, Perinatal Period - Conditions Originating in Perinatal Period, Clinical Research, Pediatric, Child, Cohort Studies, Exome, Family, Female, Humans, Parents, Pregnancy, Prenatal Diagnosis, Exome Sequencing, Paediatrics and Reproductive Medicine, Obstetrics & Reproductive Medicine, Clinical sciences, Reproductive medicine

الوصف: ObjectiveWe aimed to determine the frequency of accepting secondary findings in families undergoing exome sequencing in prenatal and pediatric settings.MethodsThis was a secondary analysis of prospectively enrolled patients undergoing trio exome sequencing for congenital anomalies or developmental disorders in prenatal and pediatric settings, in which families were offered receiving secondary findings (initially assessed in the proband and, if identified, then in the parents). The primary outcome was frequency of accepting secondary findings. Secondary outcomes included frequency of acceptance in prenatal versus pediatric settings, and sociodemographic differences between those who accepted versus declined secondary findings.ResultsThere were 682 families included in the cohort (289 prenatal and 393 pediatric). Overall, 84% (576/682) of families accepted secondary findings: 86.2% (249/289) of families undergoing prenatal versus 83.2% (327/393) pediatric (p = 0.30) testing. Secondary findings were identified in 2.6% (15/576) of cases, with no difference between prenatal and pediatric settings. There were no differences in sociodemographics between families that accepted versus declined secondary findings.ConclusionThe majority of families undergoing exome sequencing accepted secondary findings; this did not differ in prenatal versus pediatric settings. This highlights the need for guidance surrounding the offer of secondary findings in the prenatal setting.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/89h179r4Test

المؤلفون: Slavotinek, Anne M., Thompson, Michelle L., Martin, Lisa J., Gelb, Bruce D.

المساهمون: National Human Genome Research Institute, National Institutes of Health

المصدر: Human Genetics and Genomics Advances ; volume 5, issue 3, page 100286 ; ISSN 2666-2477

مصطلحات موضوعية: Genetics (clinical), Molecular Medicine

الإتاحة: https://doi.org/10.1016/j.xhgg.2024.100286Test
https://api.elsevier.com/content/article/PII:S2666247724000253?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S2666247724000253?httpAccept=text/plainTest

المؤلفون: Phillips, Kathryn A, Trosman, Julia R, Douglas, Michael P, Gelb, Bruce D, Ferket, Bart S, Hindorff, Lucia A, Slavotinek, Anne M, Berg, Jonathan S, Russell, Heidi V, Devine, Beth, Greve, Veronica, Smith, Hadley Stevens

المصدر: Genetics in Medicine. 24(1)

مصطلحات موضوعية: Clinical Research, Genetics, Human Genome, Good Health and Well Being, Base Sequence, Chromosome Mapping, Exome, Humans, Insurance Coverage, Exome Sequencing, Clinical Sciences, Genetics & Heredity

الوصف: PurposeThere is limited payer coverage for genome sequencing (GS) relative to exome sequencing (ES) in the U.S. Our objective was to assess payers' considerations for coverage of GS versus coverage of ES and requirements payers have for coverage of GS. The study was conducted by the NIH-funded Clinical Sequencing Evidence-Generating Research Consortium (CSER).MethodsWe conducted semi-structured interviews with representatives of private payer organizations (payers, N = 12) on considerations and evidentiary and other needs for coverage of GS and ES. Data were analyzed using thematic analysis.ResultsWe described four categories of findings and solutions: demonstrated merits of GS versus ES, enhanced methods for evidence generation, consistent laboratory processes/sequencing methods, and enhanced implementation/care delivery. Payers see advantages to GS vs. ES and are open to broader GS coverage but need more proof of these advantages to consider them in coverage decision-making. Next steps include establishing evidence of benefits in specific clinical scenarios, developing quality standards, ensuring transparency of laboratory methods, developing clinical centers of excellence, and incorporating the role of genetic professionals.ConclusionBy comparing coverage considerations for GS and ES, we identified a path forward for coverage of GS. Future research should explicitly address payers' conditions for coverage.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/40k972djTest

المؤلفون: Sparks, Teresa N, Lianoglou, Billie R, Adami, Rebecca R, Pluym, Ilina D, Holliman, Kerry, Duffy, Jennifer, Downum, Sarah L, Patel, Sachi, Faubel, Amanda, Boe, Nina M, Field, Nancy T, Murphy, Aisling, Laurent, Louise C, Jolley, Jennifer, Uy, Cherry, Slavotinek, Anne M, Devine, Patrick, Hodoglugil, Ugur, van Ziffle, Jessica, Sanders, Stephan J, MacKenzie, Tippi C, Norton, Mary E

المصدر: Obstetrical & Gynecological Survey. 76(3)

مصطلحات موضوعية: Paediatrics and Reproductive Medicine, Obstetrics & Reproductive Medicine

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/2v62d0jgTest

المؤلفون: Biesecker, Leslie G, Adam, Margaret P, Alkuraya, Fowzan S, Amemiya, Anne R, Bamshad, Michael J, Beck, Anita E, Bennett, James T, Bird, Lynne M, Carey, John C, Chung, Brian, Clark, Robin D, Cox, Timothy C, Curry, Cynthia, Dinulos, Mary Beth Palko, Dobyns, William B, Giampietro, Philip F, Girisha, Katta M, Glass, Ian A, Graham, John M, Gripp, Karen W, Haldeman-Englert, Chad R, Hall, Bryan D, Innes, A Micheil, Kalish, Jennifer M, Keppler-Noreuil, Kim M, Kosaki, Kenjiro, Kozel, Beth A, Mirzaa, Ghayda M, Mulvihill, John J, Nowaczyk, Malgorzata JM, Pagon, Roberta A, Retterer, Kyle, Rope, Alan F, Sanchez-Lara, Pedro A, Seaver, Laurie H, Shieh, Joseph T, Slavotinek, Anne M, Sobering, Andrew K, Stevens, Cathy A, Stevenson, David A, Tan, Tiong Yang, Tan, Wen-Hann, Tsai, Anne C, Weaver, David D, Williams, Marc S, Zackai, Elaine, Zarate, Yuri A

المصدر: American Journal of Human Genetics. 108(1)

مصطلحات موضوعية: Rare Diseases, Genetics, Cystic Fibrosis, Cystic Fibrosis Transmembrane Conductance Regulator, Genetic Diseases, Inborn, Genomics, Genotype, Humans, Mutation, Phenotype, Biological Sciences, Medical and Health Sciences, Genetics & Heredity

الوصف: The delineation of disease entities is complex, yet recent advances in the molecular characterization of diseases provide opportunities to designate diseases in a biologically valid manner. Here, we have formalized an approach to the delineation of Mendelian genetic disorders that encompasses two distinct but inter-related concepts: (1) the gene that is mutated and (2) the phenotypic descriptor, preferably a recognizably distinct phenotype. We assert that only by a combinatorial or dyadic approach taking both of these attributes into account can a unitary, distinct genetic disorder be designated. We propose that all Mendelian disorders should be designated as "GENE-related phenotype descriptor" (e.g., "CFTR-related cystic fibrosis"). This approach to delineating and naming disorders reconciles the complexity of gene-to-phenotype relationships in a simple and clear manner yet communicates the complexity and nuance of these relationships.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/14k5b9qxTest

المؤلفون: Islam, Farrah, Htun, Stephanie, Lai, Li‐Wen, Krall, Max, Poranki, Menitha, Martin, Pierre‐Marie, Sobreira, Nara, Wohler, Elizabeth S, Yu, Jingwei, Moore, Anthony T, Slavotinek, Anne M

المصدر: Clinical Genetics. 98(5)

مصطلحات موضوعية: Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Research, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Anophthalmos, Calcium-Binding Proteins, Cation Transport Proteins, Cell Adhesion Molecules, Coloboma, Consanguinity, Exome, Female, High-Throughput Nucleotide Sequencing, Humans, Kinesins, Male, Membrane Proteins, Microphthalmos, Mitochondrial Membrane Transport Proteins, Mutation, Nerve Tissue Proteins, Polymorphism, Single Nucleotide, Tumor Suppressor Proteins, Exome Sequencing, Anophthalmia, cataract, CDON, Microphthalmia, TENM3, Clinical Sciences, Genetics & Heredity, Clinical sciences

الوصف: Next-generation sequencing strategies have resulted in mutation detection rates of 21% to 61% in small cohorts of patients with microphthalmia, anophthalmia and coloboma (MAC), but despite progress in identifying novel causative genes, many patients remain without a genetic diagnosis. We studied a cohort of 19 patients with MAC who were ascertained from a population with high rates of consanguinity. Using single nucleotide polymorphism (SNP) arrays and whole exome sequencing (WES), we identified one pathogenic variant in TENM3 in a patient with cataracts in addition to MAC. We also detected novel variants of unknown significance in genes that have previously been associated with MAC, including KIF26B, MICU1 and CDON, and identified variants in candidate genes for MAC from the Wnt signaling pathway, comprising LRP6, WNT2B and IQGAP1, but our findings do not prove causality. Plausible variants were not found for many of the cases, indicating that our current understanding of the pathogenesis of MAC, a highly heterogeneous group of ocular defects, remains incomplete.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/9pk8m065Test

المؤلفون: Sparks, Teresa N, Lianoglou, Billie R, Adami, Rebecca R, Pluym, Ilina D, Holliman, Kerry, Duffy, Jennifer, Downum, Sarah L, Patel, Sachi, Faubel, Amanda, Boe, Nina M, Field, Nancy T, Murphy, Aisling, Laurent, Louise C, Jolley, Jennifer, Uy, Cherry, Slavotinek, Anne M, Devine, Patrick, Hodoglugil, Ugur, Van Ziffle, Jessica, Sanders, Stephan J, MacKenzie, Tippi C, Norton, Mary E

المصدر: New England Journal of Medicine. 383(18)

مصطلحات موضوعية: Reproductive Medicine, Biomedical and Clinical Sciences, Health Sciences, Brain Disorders, Genetics, Pediatric, Clinical Research, Human Genome, Genetic Testing, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Reproductive health and childbirth, Good Health and Well Being, Female, Genetic Variation, Humans, Hydrops Fetalis, Pregnancy, Prenatal Diagnosis, Prognosis, Exome Sequencing, University of California Fetal–Maternal Consortium, University of California, San Francisco Center for Maternal–Fetal Precision Medicine, Medical and Health Sciences, General & Internal Medicine, Biomedical and clinical sciences, Health sciences

الوصف: BackgroundThe cause of most fetal anomalies is not determined prenatally. Exome sequencing has transformed genetic diagnosis after birth, but its usefulness for prenatal diagnosis is still emerging. Nonimmune hydrops fetalis (NIHF), a fetal abnormality that is often lethal, has numerous genetic causes; the extent to which exome sequencing can aid in its diagnosis is unclear.MethodsWe evaluated a series of 127 consecutive unexplained cases of NIHF that were defined by the presence of fetal ascites, pleural or pericardial effusions, skin edema, cystic hygroma, increased nuchal translucency, or a combination of these conditions. The primary outcome was the diagnostic yield of exome sequencing for detecting genetic variants that were classified as either pathogenic or likely pathogenic according to the criteria of the American College of Medical Genetics and Genomics. Secondary outcomes were the percentage of cases associated with specific genetic disorders and the proportion of variants that were inherited.ResultsIn 37 of the 127 cases (29%), we identified diagnostic genetic variants, including those for disorders affecting the RAS-MAPK cell-signaling pathway (known as RASopathies) (30% of the genetic diagnoses); inborn errors of metabolism and musculoskeletal disorders (11% each); lymphatic, neurodevelopmental, cardiovascular, and hematologic disorders (8% each); and others. Prognoses ranged from a relatively mild outcome to death during the perinatal period. Overall, 68% of the cases (25 of 37) with diagnostic variants were autosomal dominant (of which 12% were inherited and 88% were de novo), 27% (10 of 37) were autosomal recessive (of which 95% were inherited and 5% were de novo), 1 was inherited X-linked recessive, and 1 was of uncertain inheritance. We identified potentially diagnostic variants in an additional 12 cases.ConclusionsIn this large case series of 127 fetuses with unexplained NIHF, we identified a diagnostic genetic variant in approximately one third of the cases. (Funded by the UCSF Center for Maternal-Fetal Precision Medicine and others; ClinicalTrials.gov number, NCT03412760.).

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/1kf0c1jqTest

المؤلفون: Mendelsohn, Bryce A, Beleford, Daniah T, Abu‐El‐Haija, Aya, Alsaleh, Norah S, Rahbeeni, Zuhair, Martin, Pierre‐Marie, Rego, Shannon, Huang, Alyssa, Capodanno, Gina, Shieh, Joseph T, Van Ziffle, Jessica, Risch, Neil, Alkuraya, Fowzan S, Slavotinek, Anne M

المصدر: American Journal of Medical Genetics Part A. 182(3)

مصطلحات موضوعية: Pediatric, Rare Diseases, Brain Disorders, Congenital Structural Anomalies, Aetiology, 2.1 Biological and endogenous factors, Child, Child, Preschool, DNA-Binding Proteins, Female, Genetic Association Studies, Genetic Diseases, X-Linked, Genetic Predisposition to Disease, Humans, Male, Mutation, Trichothiodystrophy Syndromes, X Chromosome Inactivation, RNF113A, spliceosome, trichothiodystrophy, zinc finger, RNF113A, Genetics, Clinical Sciences

الوصف: We describe an 11-year old boy with severe global developmental delays, failure to thrive and growth retardation, refractory seizures with recurrent status epilepticus, hypogammaglobulinemia, hypergonadotropic hypogonadism, and duodenal strictures. He had facial and skin findings compatible with trichothiodystrophy, including sparse and brittle hair, thin eyebrows, and dry skin. Exome sequencing showed a hemizygous, truncating variant in RNF113A, c.903_910delGCAGACCA, predicting p.(Gln302fs*12), that was inherited from his mother. Although his clinical features overlap closely with features described in the two previously reported male first cousins with RNF113A loss of function mutations, the duodenal strictures seen in this patient have not been reported. Interestingly, the patient's mother had short stature and 100% skewed X-inactivation as seen in other obligate female carriers. A second male with developmental delays, microcephaly, seizures, ambiguous genitalia, and facial anomalies that included sparse and brittle hair, thin eyebrows and dry skin was recently reported to have c.897_898delTG, predicting p.(Cys299*) in RNF113A and we provide additional clinical details for this patient. This report further supports deleterious variants in RNF113A as a cause of a novel trichothiodystrophy syndrome.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/17b4j483Test

المؤلفون: Kanca, Oguz, Andrews, Jonathan C, Lee, Pei-Tseng, Patel, Chirag, Braddock, Stephen R, Slavotinek, Anne M, Cohen, Julie S, Gubbels, Cynthia S, Aldinger, Kimberly A, Williams, Judy, Indaram, Maanasa, Fatemi, Ali, Yu, Timothy W, Agrawal, Pankaj B, Vezina, Gilbert, Simons, Cas, Crawford, Joanna, Lau, C Christopher, Undiagnosed Diseases Network, Chung, Wendy K, Markello, Thomas C, Dobyns, William B, Adams, David R, Gahl, William A, Wangler, Michael F, Yamamoto, Shinya, Bellen, Hugo J, Malicdan, May Christine V

المصدر: American journal of human genetics. 105(2)

مصطلحات موضوعية: Undiagnosed Diseases Network, Cerebellum, Animals, Humans, Drosophila melanogaster, Epilepsy, Nervous System Malformations, Coloboma, Microfilament Proteins, Developmental Disabilities, Amino Acid Sequence, Sequence Homology, Phenotype, Mutation, Adult, Child, Infant, Infant, Newborn, Female, Male, Young Adult, Body Dysmorphic Disorders, Intellectual Disability, WD40 Repeats, CG12333, Drosophila, WD40 repeats, WDR37 domains, bang sensitivity, wdr37, Genetics, Pediatric, Rare Diseases, Congenital Structural Anomalies, Neurodegenerative, Neurosciences, Brain Disorders, Intellectual and Developmental Disabilities (IDD), Aetiology, 2.1 Biological and endogenous factors, Neurological, Biological Sciences, Medical and Health Sciences, Genetics & Heredity

الوصف: WD40 repeat-containing proteins form a large family of proteins present in all eukaryotes. Here, we identified five pediatric probands with de novo variants in WDR37, which encodes a member of the WD40 repeat protein family. Two probands shared one variant and the others have variants in nearby amino acids outside the WD40 repeats. The probands exhibited shared phenotypes of epilepsy, colobomas, facial dysmorphology reminiscent of CHARGE syndrome, developmental delay and intellectual disability, and cerebellar hypoplasia. The WDR37 protein is highly conserved in vertebrate and invertebrate model organisms and is currently not associated with a human disease. We generated a null allele of the single Drosophila ortholog to gain functional insights and replaced the coding region of the fly gene CG12333/wdr37 with GAL4. These flies are homozygous viable but display severe bang sensitivity, a phenotype associated with seizures in flies. Additionally, the mutant flies fall when climbing the walls of the vials, suggesting a defect in grip strength, and repeat the cycle of climbing and falling. Similar to wall clinging defect, mutant males often lose grip of the female abdomen during copulation. These phenotypes are rescued by using the GAL4 in the CG12333/wdr37 locus to drive the UAS-human reference WDR37 cDNA. The two variants found in three human subjects failed to rescue these phenotypes, suggesting that these alleles severely affect the function of this protein. Taken together, our data suggest that variants in WDR37 underlie a novel syndromic neurological disorder.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/8wx8g9p6Test