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For: O'Hern K, Barney R, Chambers M, Baker C, Stevanovic M, Tsongalis GJ, Hughes E, Sriharan A. A novel method to assess copy number variation in melanoma: Droplet digital PCR for precise quantitation of the RREB1 gene in formalin-fixed, paraffin-embedded melanocytic neoplasms, a proof-of-concept study. J Cutan Pathol 2023;50:169-177. [PMID: 36325821 DOI: 10.1111/cup.14352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]

For:	O'Hern K, Barney R, Chambers M, Baker C, Stevanovic M, Tsongalis GJ, Hughes E, Sriharan A. A novel method to assess copy number variation in melanoma: Droplet digital PCR for precise quantitation of the RREB1 gene in formalin-fixed, paraffin-embedded melanocytic neoplasms, a proof-of-concept study. J Cutan Pathol 2023;50:169-177. [PMID: 36325821 DOI: 10.1111/cup.14352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]

Number

Cited by Other Article(s)

McFadden JR, Salem I, Stevanovic M, Barney RE, Chaudhari AS, Chambers MA, O'Hern K, Cloutier JM, Yan S, Ramos-Rodriguez AJ, Kerr DA, Momtahen S, LeBlanc RE, Tsongalis GJ, Hughes EG, Sriharan A. A Droplet Digital Polymerase Chain Reaction-Based Tool to Aid in Melanoma Diagnosis: Development of a 4-Gene Panel Using 164 Melanocytic Neoplasms. Arch Pathol Lab Med 2025;149:410-421. [PMID: 39084636 DOI: 10.5858/arpa.2024-0027-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 08/02/2024]

Abstract

CONTEXT.—

Detecting copy number variations (CNVs) at certain loci can aid in the diagnosis of histologically ambiguous melanocytic neoplasms. Droplet digital polymerase chain reaction (ddPCR) is a rapid, automated, and inexpensive method for CNV detection in other cancers, but not yet melanoma.

OBJECTIVE.—

To evaluate the performance of a 4-gene ddPCR panel that simultaneously tests for ras responsive binding element protein 1 (RREB1) gain; cyclin-dependent kinase inhibitor 2A (CDKN2A) loss; MYC proto-oncogene, bHLH transcription factor (MYC) gain; and MYB proto-oncogene, transcription factor (MYB) loss in melanocytic neoplasms.

DESIGN.—

One hundred sixty-four formalin-fixed, paraffin-embedded skin samples were used to develop the assay, of which 65 were used to evaluate its performance. Chromosomal microarray analysis (CMA) data were used as the gold standard.

RESULTS.—

ddPCR demonstrated high concordance with CMA in detecting RREB1 gain (sensitivity, 86.7%; specificity, 88.9%), CDKN2A loss (sensitivity, 80%; specificity, 100%), MYC gain (sensitivity, 70%; specificity, 100%), and MYB loss (sensitivity, 71.4%; specificity, 100%). When one CNV was required to designate the test as positive, the 4-gene ddPCR panel distinguished nevi from melanomas with a sensitivity of 78.4% and a specificity of 71.4%. For reference, CMA had a sensitivity of 86.2% and a specificity of 78.6%. Our data also revealed interesting relationships with histology, namely (1) a positive correlation between RREB1 ddPCR copy number and degree of tumor progression; (2) a statistically significant correlation between MYC gain and nodular growth; and (3) a statistically significant correlation between MYB loss and a sheetlike pattern of growth.

CONCLUSIONS.—

With further validation, ddPCR may aid both in our understanding of melanomagenesis and in the diagnosis of challenging melanocytic neoplasms.

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Affiliation(s)

Jason R McFadden From the Department of Biological Sciences (McFadden, Chaudhari), and the Geisel School of Medicine (Stevanovic, Kerr, Tsongalis, Sriharan), Dartmouth College, Hanover, New Hampshire
Iman Salem the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Mirjana Stevanovic From the Department of Biological Sciences (McFadden, Chaudhari), and the Geisel School of Medicine (Stevanovic, Kerr, Tsongalis, Sriharan), Dartmouth College, Hanover, New Hampshire
Rachael E Barney the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Advaita S Chaudhari From the Department of Biological Sciences (McFadden, Chaudhari), and the Geisel School of Medicine (Stevanovic, Kerr, Tsongalis, Sriharan), Dartmouth College, Hanover, New Hampshire
Meagan Ann Chambers the Department of Pathology and Laboratory Medicine, University of Washington, Seattle (Chambers)
Keegan O'Hern the Department of Dermatology, Mayo Clinic, Rochester, Minnesota (O'Hern)
Jeffrey M Cloutier the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Shaofeng Yan the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Alvaro J Ramos-Rodriguez the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Darcy Arendt Kerr From the Department of Biological Sciences (McFadden, Chaudhari), and the Geisel School of Medicine (Stevanovic, Kerr, Tsongalis, Sriharan), Dartmouth College, Hanover, New Hampshire the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Shabnam Momtahen the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Robert E LeBlanc the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Gregory J Tsongalis From the Department of Biological Sciences (McFadden, Chaudhari), and the Geisel School of Medicine (Stevanovic, Kerr, Tsongalis, Sriharan), Dartmouth College, Hanover, New Hampshire the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Edward G Hughes the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
Aravindhan Sriharan From the Department of Biological Sciences (McFadden, Chaudhari), and the Geisel School of Medicine (Stevanovic, Kerr, Tsongalis, Sriharan), Dartmouth College, Hanover, New Hampshire the Departments of Dermatology (Salem) and Pathology & Laboratory Medicine (Barney, Cloutier, Yan, Ramos-Rodriguez, Kerr, Momtahen, LeBlanc, Tsongalis, Hughes, Sriharan), Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire

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Grebnev PA, Meshkov IO, Ershov PV, Makhotenko AV, Azarian VB, Erokhina MV, Galeta AA, Zakubanskiy AV, Shingalieva OS, Tregubova AV, Asaturova AV, Yudin VS, Yudin SM, Makarov VV, Keskinov AA, Makarova AS, Snigir EA, Skvortsova VI. Benchmarking of Approaches for Gene Copy-Number Variation Analysis and Its Utility for Genetic Aberration Detection in High-Grade Serous Ovarian Carcinomas. Cancers (Basel) 2024;16:3252. [PMID: 39409874 PMCID: PMC11475927 DOI: 10.3390/cancers16193252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 09/20/2024] [Accepted: 09/21/2024] [Indexed: 10/20/2024] Open

Affiliation(s)

Pavel Alekseevich Grebnev Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Ivan Olegovich Meshkov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Pavel Viktorovich Ershov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Antonida Viktorovna Makhotenko Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Valentina Bogdanovna Azarian Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Marina Vyacheslavovna Erokhina Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anastasiya Aleksandrovna Galeta Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Aleksandr Vladimirovich Zakubanskiy Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Olga Sergeevna Shingalieva Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anna Vasilevna Tregubova Federal State Budgetary Institution “National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov”, Ministry of Healthcare of The Russian Federation, Oparina Street, Bld. 4, 117997 Moscow, Russia; (A.V.T.); (A.V.A.)
Aleksandra Vyacheslavovna Asaturova Federal State Budgetary Institution “National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov”, Ministry of Healthcare of The Russian Federation, Oparina Street, Bld. 4, 117997 Moscow, Russia; (A.V.T.); (A.V.A.)
Vladimir Sergeevich Yudin Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Sergey Mihaylovich Yudin Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Valentin Vladimirovich Makarov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anton Arturovich Keskinov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anna Sergeevna Makarova Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Ekaterina Andreevna Snigir Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Veronika Igorevna Skvortsova Federal Medical Biological Agency (FMBA of Russia), Volokolamskoye Shosse, 30, 123182 Moscow, Russia;

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Ramos-Rodriguez AJ, McFadden JR, Momtahen S, LeBlanc RE, Yan S, Chaudhari AS, Cloutier JM, Stevanovic M, Barney R, Syku M, Lozano-Franco M, Hughes E, Sriharan A. A novel method to assess copy number variations in melanocytic neoplasms: Droplet digital PCR for precise quantitation of MYC and MYB genes. J Cutan Pathol 2024;51:146-154. [PMID: 37795541 PMCID: PMC10863652 DOI: 10.1111/cup.14540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]

Griffin EN, Jucius T, Sim SE, Harris BS, Heinz S, Ackerman SL. RREB1 regulates neuronal proteostasis and the microtubule network. SCIENCE ADVANCES 2024;10:eadh3929. [PMID: 38198538 PMCID: PMC10780896 DOI: 10.1126/sciadv.adh3929] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]

Kakumanu ML, Hickin ML, Schal C. Detection, Quantification, and Elimination of Wolbachia in Bed Bugs. Methods Mol Biol 2024;2739:97-114. [PMID: 38006547 PMCID: PMC11583902 DOI: 10.1007/978-1-0716-3553-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]