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Year Number of Results
2018 10
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2020 17
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2022 22
2023 14

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Page 1
Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria.
Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS, Biesecker LG, Radivojac P, Brenner SE; ClinGen Sequence Variant Interpretation Working Group. Pejaver V, et al. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. doi: 10.1016/j.ajhg.2022.10.013. Epub 2022 Nov 21. Am J Hum Genet. 2022. PMID: 36413997 Free PMC article.
We have extended this framework to computational predictors and introduce a new standard that converts a tool's scores to PP3 and BP4 evidence strengths. Our approach is based on estimating the local positive predictive value and can calibrate any computational tool or oth …
We have extended this framework to computational predictors and introduce a new standard that converts a tool's scores to PP3 and BP4 …
Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework.
Brnich SE, Abou Tayoun AN, Couch FJ, Cutting GR, Greenblatt MS, Heinen CD, Kanavy DM, Luo X, McNulty SM, Starita LM, Tavtigian SV, Wright MW, Harrison SM, Biesecker LG, Berg JS; Clinical Genome Resource Sequence Variant Interpretation Working Group. Brnich SE, et al. Genome Med. 2019 Dec 31;12(1):3. doi: 10.1186/s13073-019-0690-2. Genome Med. 2019. PMID: 31892348 Free PMC article.
ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines.
Preston CG, Wright MW, Madhavrao R, Harrison SM, Goldstein JL, Luo X, Wand H, Wulf B, Cheung G, Mandell ME, Tong H, Cheng S, Iacocca MA, Pineda AL, Popejoy AB, Dalton K, Zhen J, Dwight SS, Babb L, DiStefano M, O'Daniel JM, Lee K, Riggs ER, Zastrow DB, Mester JL, Ritter DI, Patel RY, Subramanian SL, Milosavljevic A, Berg JS, Rehm HL, Plon SE, Cherry JM, Bustamante CD, Costa HA; Clinical Genome Resource (ClinGen). Preston CG, et al. Genome Med. 2022 Jan 18;14(1):6. doi: 10.1186/s13073-021-01004-8. Genome Med. 2022. PMID: 35039090 Free PMC article.
Parent-Reported Clinical Utility of Pediatric Genomic Sequencing.
Smith HS, Ferket BS, Gelb BD, Hindorff L, Ferar KD, Norton ME, Sahin-Hodoglugil N, Slavotinek A, Lich KH, Berg JS, Russell HV. Smith HS, et al. Pediatrics. 2023 Aug 1;152(2):e2022060318. doi: 10.1542/peds.2022-060318. Pediatrics. 2023. PMID: 37470118
We assessed clinicians' recommendations after GS, parent-reported follow-up, and actions parents initiated in response to learning their child's GS results. METHODS: We surveyed parents of children who received GS through the Clinical Sequencing Evidence Generating Researc …
We assessed clinicians' recommendations after GS, parent-reported follow-up, and actions parents initiated in response to learning their chi …
FDA oversight of NSIGHT genomic research: the need for an integrated systems approach to regulation.
Milko LV, Chen F, Chan K, Brower AM, Agrawal PB, Beggs AH, Berg JS, Brenner SE, Holm IA, Koenig BA, Parad RB, Powell CM, Kingsmore SF. Milko LV, et al. NPJ Genom Med. 2019 Dec 10;4:32. doi: 10.1038/s41525-019-0105-8. eCollection 2019. NPJ Genom Med. 2019. PMID: 31839987 Free PMC article. Review.
Here, we review the history of and rationale behind FDA oversight of clinical research and the NSIGHT Consortium's experiences in navigating the IDE process. Overall, NSIGHT investigators found that FDA's application of existing IDE regulations and medical device de …
Here, we review the history of and rationale behind FDA oversight of clinical research and the NSIGHT Consortium's experiences in nav …
Genomic Sequencing for Newborn Screening: Results of the NC NEXUS Project.
Roman TS, Crowley SB, Roche MI, Foreman AKM, O'Daniel JM, Seifert BA, Lee K, Brandt A, Gustafson C, DeCristo DM, Strande NT, Ramkissoon L, Milko LV, Owen P, Roy S, Xiong M, Paquin RS, Butterfield RM, Lewis MA, Souris KJ, Bailey DB Jr, Rini C, Booker JK, Powell BC, Weck KE, Powell CM, Berg JS. Roman TS, et al. Am J Hum Genet. 2020 Oct 1;107(4):596-611. doi: 10.1016/j.ajhg.2020.08.001. Epub 2020 Aug 26. Am J Hum Genet. 2020. PMID: 32853555 Free PMC article.
We enrolled healthy newborns and children with metabolic diseases or hearing loss (106 participants total). ES confirmed the participant's underlying diagnosis in 15 out of 17 (88%) children with metabolic disorders and in 5 out of 28 (18%) children with hearing loss. ...
We enrolled healthy newborns and children with metabolic diseases or hearing loss (106 participants total). ES confirmed the participant' …
The Burden of COVID-19 on Caregivers of Children with Suspected Genetic Conditions: A Therapeutic Odyssey.
Waltz M, Canter C, Bensen JT, Berg JS, Foreman AKM, Grant TL, Hassmiller Lich K, Navas A, O'Daniel JM, Powell BC, Rini CM, Staley BS, Cadigan RJ. Waltz M, et al. Phys Occup Ther Pediatr. 2023;43(3):257-271. doi: 10.1080/01942638.2022.2138734. Epub 2022 Oct 30. Phys Occup Ther Pediatr. 2023. PMID: 36310386
RESULTS: Most caregivers did not report any interruptions to their child's diagnostic odyssey. The greatest impact was access to therapy services, including the suspension or loss of their child's in-person therapeutic care and difficulties with virtual therapies. . …
RESULTS: Most caregivers did not report any interruptions to their child's diagnostic odyssey. The greatest impact was access to ther …
Chromium Cycling in Redox-Stratified Basins Challenges δ53Cr Paleoredox Proxy Applications.
Janssen DJ, Rickli J, Wille M, Sepúlveda Steiner O, Vogel H, Dellwig O, Berg JS, Bouffard D, Lever MA, Hassler CS, Jaccard SL. Janssen DJ, et al. Geophys Res Lett. 2022 Nov 16;49(21):e2022GL099154. doi: 10.1029/2022GL099154. Epub 2022 Oct 28. Geophys Res Lett. 2022. PMID: 36589775 Free PMC article.
Chromium stable isotope composition (delta(53)Cr) is a promising tracer for redox conditions throughout Earth's history; however, the geochemical controls of delta(53)Cr have not been assessed in modern redox-stratified basins. ...
Chromium stable isotope composition (delta(53)Cr) is a promising tracer for redox conditions throughout Earth's history; however, the …
Rapid pyritization in the presence of a sulfur/sulfate-reducing bacterial consortium.
Berg JS, Duverger A, Cordier L, Laberty-Robert C, Guyot F, Miot J. Berg JS, et al. Sci Rep. 2020 May 19;10(1):8264. doi: 10.1038/s41598-020-64990-6. Sci Rep. 2020. PMID: 32427954 Free PMC article.
Our results suggest that rates of pyritization vs. vivianite formation are regulated by SRB activity at the cellular scale, which enhances phosphate release into the aqueous phase by increased efficiency of iron sulfide precipitation, and thus that these microorganisms strongly i …
Our results suggest that rates of pyritization vs. vivianite formation are regulated by SRB activity at the cellular scale, which enhances p …
75 results