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Wyrwoll MJ, Wabschke R, Röpke A, Wöste M, Ruckert C, Perrey S, Rotte N, Hardy J, Astica L, Lupiáñez DG, Wistuba J, Westernströer B, Schlatt S, Berman AJ, Müller AM, Kliesch S, Yatsenko AN, Tüttelmann F, Friedrich C. Analysis of copy number variation in men with non-obstructive azoospermia. Andrology 2022; 10:1593-1604. [PMID: 36041235 PMCID: PMC9605881 DOI: 10.1111/andr.13267] [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: 01/20/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Recent findings demonstrate that single nucleotide variants can cause non-obstructive azoospermia (NOA). In contrast, copy number variants (CNVs) were only analysed in few studies in infertile men. Some have reported a higher prevalence of CNVs in infertile versus fertile men. OBJECTIVES This study aimed to elucidate if CNVs are associated with NOA. MATERIALS AND METHODS We performed array-based comparative genomic hybridisation (aCGH) in 37 men with meiotic arrest, 194 men with Sertoli cell-only phenotype, and 21 control men. We filtered our data for deletions affecting genes and prioritised the affected genes according to the literature search. Prevalence of CNVs was compared between all groups. Exome data of 2,030 men were screened to detect further genetic variants in prioritised genes. Modelling was performed for the protein encoded by the novel candidate gene TEKT5 and we stained for TEKT5 in human testicular tissue. RESULTS We determined the cause of infertility in two individuals with homozygous deletions of SYCE1 and in one individual with a heterozygous deletion of SYCE1 combined with a likely pathogenic missense variant on the second allele. We detected heterozygous deletions affecting MLH3, EIF2B2, SLX4, CLPP and TEKT5, in one subject each. CNVs were not detected more frequently in infertile men compared with controls. DISCUSSION While SYCE1 and MLH3 encode known meiosis-specific proteins, much less is known about the proteins encoded by the other identified candidate genes, warranting further analyses. We were able to identify the cause of infertility in one out of the 231 infertile men by aCGH and in two men by using exome sequencing data. CONCLUSION As aCGH and exome sequencing are both expensive methods, combining both in a clinical routine is not an effective strategy. Instead, using CNV calling from exome data has recently become more precise, potentially making aCGH dispensable.
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Affiliation(s)
- M. J. Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - R. Wabschke
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - A. Röpke
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - M. Wöste
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - C. Ruckert
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - S. Perrey
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, Recklinghausen, Germany
| | - N. Rotte
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - J. Hardy
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Women Research Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - L. Astica
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - D. G. Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - J. Wistuba
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - B. Westernströer
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - S. Schlatt
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - A. J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - A. M. Müller
- Practice for Pathology and Centre for Pediatric Pathology, University Hospital of Cologne, Cologne, Germany
| | - S. Kliesch
- Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - A. N. Yatsenko
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Women Research Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - F. Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - C. Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
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Hardy J, Pollock N, Gingrich T, Sweet P, Ramesh A, Kuong J, Basar A, Jiang H, Hwang K, Vukina J, Jaffe T, Olszewska M, Kurpisz M, Yatsenko AN. Genomic testing for copy number and single nucleotide variants in spermatogenic failure. J Assist Reprod Genet 2022; 39:2103-2114. [PMID: 35849255 PMCID: PMC9474750 DOI: 10.1007/s10815-022-02538-5] [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: 02/16/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022] Open
Abstract
PURPOSE To identify clinically significant genomic copy number (CNV) and single nucleotide variants (SNV) in males with unexplained spermatogenic failure (SPGF). MATERIALS AND METHODS Peripheral blood DNA from 97/102 study participants diagnosed with oligozoospermia, severe oligozoospermia, or non-obstructive azoospermia (NOA) was analyzed for CNVs via array comparative genomic hybridization (aCGH) and SNVs using whole-exome sequencing (WES). RESULTS Of the 2544 CNVs identified in individuals with SPGF, > 90% were small, ranging from 0.6 to 75 kb. Thirty, clinically relevant genomic aberrations, were detected in 28 patients (~ 29%). These included likely diagnostic CNVs in 3/41 NOA patients (~ 7%): 1 hemizygous, intragenic TEX11 deletion, 1 hemizygous DDX53 full gene deletion, and 1 homozygous, intragenic STK11 deletion. High-level mosaicism for X chromosome disomy (~ 10% 46,XY and ~ 90% 47,XXY) was also identified in 3 of 41 NOA patients who previously tested normal with conventional karyotyping. The remaining 24 CNVs detected were heterozygous, autosomal recessive carrier variants. Follow-up WES analysis confirmed 8 of 27 (30%) CNVs (X chromosome disomy excluded). WES analysis additionally identified 13 significant SNVs and/or indels in 9 patients (~ 9%) including X-linked AR, KAL1, and NR0B1 variants. CONCLUSION Using a combined genome-wide aCGH/WES approach, we identified pathogenic and likely pathogenic SNVs and CNVs in 15 patients (15%) with unexplained SPGF. This value equals the detection rate of conventional testing for aneuploidies and is considerably higher than the prevalence of Y chromosome microdeletions. Our results underscore the importance of comprehensive genomic analysis in emerging diagnostic testing of complex conditions like male infertility.
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Affiliation(s)
- J Hardy
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - N Pollock
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - T Gingrich
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - P Sweet
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - A Ramesh
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - J Kuong
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - A Basar
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - H Jiang
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - K Hwang
- Department of Urology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - J Vukina
- Department of Urology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - T Jaffe
- Department of Urology, School of Medicine, West Virginia University, Morgantown, WV, USA
| | - M Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - M Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - A N Yatsenko
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA.
- Department of Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States.
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.
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Yatsenko SA, Bakos HA, Vitullo K, Kedrov M, Kishore A, Jennings BJ, Surti U, Wood-Trageser MA, Cercone S, Yatsenko AN, Rajkovic A, Iannaccone A. High-resolution microarray analysis unravels complex Xq28 aberrations in patients and carriers affected by X-linked blue cone monochromacy. Clin Genet 2015; 89:82-7. [PMID: 26153062 DOI: 10.1111/cge.12638] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 05/13/2015] [Revised: 06/15/2015] [Accepted: 07/06/2015] [Indexed: 11/30/2022]
Abstract
The human X chromosome contains ∼ 1600 genes, about 15% of which have been associated with a specific genetic condition, mainly affecting males. Blue cone monochromacy (BCM) is an X-linked condition caused by a loss-of-function of both the OPN1LW and OPN1MW opsin genes. The cone opsin gene cluster is composed of 2-9 paralogs with 99.8% sequence homology and is susceptible to deletions, duplications, and mutations. Current diagnostic tests employ polymerase chain reaction (PCR)-based technologies; however, alterations remain undetermined in 10% of patients. Furthermore, carrier testing in females is limited or unavailable. High-resolution X chromosome-targeted CGH microarray was applied to test for rearrangements in males with BCM and female carriers from three unrelated families. Pathogenic alterations were revealed in all probands, characterized by sequencing of the breakpoint junctions and quantitative real-time PCR. In two families, we identified a novel founder mutation that consisted of a complex 3-kb deletion that embraced the cis-regulatory locus control region and insertion of an additional aberrant OPN1MW gene. The application of high-resolution X-chromosome microarray in clinical diagnosis brings significant advantages in detection of small aberrations that are beyond the resolution of clinically available aCGH analysis and which can improve molecular diagnosis of the known conditions and unravel previously unrecognized X-linked diseases.
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Affiliation(s)
- S A Yatsenko
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - H A Bakos
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA
| | - K Vitullo
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA
| | - M Kedrov
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, USA
| | - A Kishore
- Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh, PA, USA
| | - B J Jennings
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, USA
| | - U Surti
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - M A Wood-Trageser
- Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh, PA, USA
| | - S Cercone
- Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh, PA, USA
| | - A N Yatsenko
- Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - A Rajkovic
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - A Iannaccone
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, USA
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Lynch C, Tee N, Rouse H, Gordon A, Sati L, Zeiss C, Soygur B, Bassorgun I, Goksu E, Demir R, McGrath J, Groendahl ML, Thuesen L, Andersen AN, Loft A, Smitz J, Adriaenssens T, Vikesa J, Borup R, Mersy E, Kisters N, Macville MVE, Engelen JJM, Consortium SENN, Menheere PPCA, Geraedts JP, Coumans ABC, Frints SGM, Aledani T, Assou S, Traver S, Ait-ahmed O, Dechaud H, Hamamah S, Mizutani E, Suzumori N, Sugiyama C, Hattori Y, Sato T, Ando H, Ozaki Y, Sugiura-Ogasawara M, Wissing M, Kristensen SG, Andersen CY, Mikkelsen AL, Hoest T, Borup R, Groendahl ML, Velthut-Meikas A, Simm J, Metsis M, Salumets A, Palini S, Galluzzi L, De Stefani S, Primiterra M, Wells D, Magnani M, Bulletti C, Vogt PH, Frank-Herrmann P, Bender U, Strowitzki T, Besikoglu B, Heidemann P, Wunsch L, Bettendorf M, Jelinkova L, Vilimova S, Kosarova M, Sebek P, Volemanova E, Kruzelova M, Civisova J, Svobodova L, Sobotka V, Mardesic T, van de Werken C, Santos MA, Eleveld C, Laven JSE, Baart EB, Pylyp LY, Spinenko LA, Zukin VD, Perez-Sanz J, Matorras R, Arluzea J, Bilbao J, Gonzalez-Santiago N, Yeh N, Koff A, Barlas A, Romin Y, Manova-Todorova K, Hoz CDL, Mauri AL, Nascimento AM, Vagnini LD, Petersen CG, Ricci J, Massaro FC, Cavagna M, Pontes A, Oliveira JBA, Baruffi RLR, Franco JG, Wu EX, Ma S, Parriego M, Sole M, Boada M, Coroleu B, Veiga A, Kakourou G, Poulou M, Vrettou C, Destouni A, Traeger-Synodinos J, Kanavakis E, Yatsenko AN, Georgiadis AP, McGuire MM, Zorrilla M, Bunce KD, Peters D, Rajkovic A, Olszewska M, Kurpisz M, Gilbertson AZA, Ottolini CS, Summers MC, Sage K, Handyside AH, Thornhill AR, Griffin DK, Chung MK, Kim JW, Lee JH, Jeong HJ, Kim MH, Ryu MJ, Park SJ, Kang HY, Lee HS, Zimmermann B, Banjevic M, Hill M, Lacroute P, Dodd M, Sigurjonsson S, Lau P, Prosen D, Chopra N, Ryan A, Hall M, McAdoo S, Demko Z, Levy B, Rabinowitz M, Vereczeky A, Kosa ZS, Savay S, Csenki M, Nanassy L, Dudas B, Domotor ZS, Debreceni D, Rossi A, Alegretti JR, Cuzzi J, Bonavita M, Tanada M, Matunaga P, Fettback P, Rosa MB, Maia V, Hassun P, Motta ELA, Piccolomini M, Gomes C, Barros B, Nicoliello M, Matunaga P, Criscuolo T, Bonavita M, Alegretti JR, Miyadahira E, Cuzzi J, Hassun P, Motta ELA, Montjean D, Benkhalifa M, Berthaut I, Griveau JF, Morcel K, Bashamboo A, McElreavey K, Ravel C, Rubio C, Rodrigo L, Mateu E, Mercader A, Peinado V, Buendia P, Milan M, Delgado A, Al-Asmar N, Escrich L, Campos-Galindo I, Garcia-Herrero S, Poo ME, Mir P, Simon C, Reyes-Engel A, Cortes-Rodriguez M, Lendinez A, Perez-Nevot B, Palomares AR, Galdon MR, Ruberti A, Minasi MG, Biricik A, Colasante A, Zavaglia D, Iammarrone E, Fiorentino F, Greco E, Demir N, Ozturk S, Sozen B, Morales R, Lledo B, Ortiz JA, Ten J, Llacer J, Bernabeu R, Nagayoshi M, Tanaka A, Tanaka I, Kusunoki H, Watanabe S, Temel SG, Beyazyurek C, Ekmekci GC, Aybar F, Cinar C, Kahraman S, Nordqvist S, Karehed K, Akerud H, Ottolini CS, Griffin DK, Thornhill AR, Handyside AH, Gultomruk M, Tulay P, Findikli N, Yagmur E, Karlikaya G, Ulug U, Bahceci M, Bargallo MF, Arevalo MR, Salat MM, Barbat IV, Lopez JT, Algam ME, Boluda AB, de Oya GC, Tolmacheva EN, Kashevarova AA, Skryabin NA, Lebedev IN, Semaco E, Belo A, Riboldi M, Cuzzi J, Barros B, Luz L, Criscuolo T, Nobrega N, Matunaga P, Mazetto R, Alegretti JA, Bibancos M, Hassun P, Motta ELA, Serafini P, Neupane J, Vandewoestyne M, Heindryckx B, Deroo T, Lu Y, Ghimire S, Lierman S, Qian C, Deforce D, De Sutter P, Rodrigo L, Rubio C, Mateu E, Peinado V, Milan M, Viloria T, Al-Asmar N, Mercader A, Buendia P, Delgado A, Escrich L, Martinez-Jabaloyas JM, Simon C, Gil-Salom M, Capalbo A, Treff N, Cimadomo D, Tao X, Ferry K, Ubaldi FM, Rienzi L, Scott RT, Katzorke N, Strowitzki T, Vogt HP, Hehr A, Gassner C, Paulmann B, Kowalzyk Z, Klatt M, Krauss S, Seifert D, Seifert B, Hehr U, Minasi MG, Ruberti A, Biricik A, Lobascio M, Zavaglia D, Varricchio MT, Fiorentino F, Greco E, Rubino P, Bono S, Cotarelo RP, Spizzichino L, Biricik A, Colicchia A, Giannini P, Fiorentino F, Suhorutshenko M, Rosenstein-Tamm K, Simm J, Salumets A, Metsis M. Reproductive (epi)genetics. Hum Reprod 2013. [DOI: 10.1093/humrep/det220] [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: 11/14/2022] Open
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