1
|
Prokurotaite E, Condorelli M, Dechene J, Bouziotis J, Lambertini M, Demeestere I. Impact of Breast Cancer and Germline BRCA Pathogenic Variants on Fertility Preservation in Young Women. Life (Basel) 2023; 13:life13040930. [PMID: 37109459 PMCID: PMC10146760 DOI: 10.3390/life13040930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Background: Several studies have suggested that breast cancer (BC) and germline BRCA pathogenic variants (gBRCA PVs) could have a deleterious impact on ovarian reserve. Nevertheless, data are limited and mixed. Our objective was to evaluate the performance of fertility preservation (FP) in terms of the number of collected mature oocytes after ovarian stimulation (OS) in young women carrying a gBRCA PV, associated or not with BC. Methods: We conducted a retrospective monocentric study at HUB-Hôpital Erasme in Brussels. All women aged between 18 and 41 years diagnosed with invasive non-metastatic BC and/or gBRCA PV carriers who underwent OS for FP or preimplantation genetic testing for monogenic disorder (PGT-M) between November 2012 and October 2021 were included. Three groups were compared: BC patients without a gBRCA PV, BC patients with a gBRCA PV, and healthy gBRCA PV carriers. Ovarian reserve was evaluated based on the efficacy of OS and AMH levels. Results: A total of 85 patients underwent 100 cycles. The mean age (32.2 ± 3.9 years; p = 0.61) and median AMH level (1.9 [0.2–13] μg/L; p = 0.22) were similar between groups. Correlations between the number of mature oocytes and AMH level (p < 0.001) and between AMH and age (p < 0.001) were observed. No differences in the number of retrieved mature oocytes were observed between groups (p = 0.41), or for other OS parameters. Conclusion: Neither BC nor a gBRCA PV significantly affects ovarian reserve and FP efficacy in terms of the number of mature oocytes retrieved.
Collapse
Affiliation(s)
- Elze Prokurotaite
- Fertility Clinic, Department of Obstetrics and Gynecology, H.U.B—Hôpital Erasme, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Margherita Condorelli
- Fertility Clinic, Department of Obstetrics and Gynecology, H.U.B—Hôpital Erasme, Université Libre de Bruxelles, 1070 Brussels, Belgium
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Julie Dechene
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Jason Bouziotis
- Department of Biomedical Research, H.U.B—Hôpital Erasme, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Matteo Lambertini
- Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, 16132 Genova, Italy
- Department of Medical Oncology, U.O. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Isabelle Demeestere
- Fertility Clinic, Department of Obstetrics and Gynecology, H.U.B—Hôpital Erasme, Université Libre de Bruxelles, 1070 Brussels, Belgium
- Research Laboratory on Human Reproduction, Université Libre de Bruxelles, 1070 Brussels, Belgium
| |
Collapse
|
2
|
Yang L, Xu Y, Xia J, Yan H, Ding C, Shi Q, Wu Y, Liu P, Pan J, Zeng Y, Zhang Y, Chen F, Jiang H, Xu Y, Li W, Zhou C, Gao Y. Simultaneous detection of genomic imbalance in patients receiving preimplantation genetic testing for monogenic diseases (PGT-M). Front Genet 2022; 13:976131. [PMID: 36246639 PMCID: PMC9559864 DOI: 10.3389/fgene.2022.976131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Preimplantation genetic test for monogenic disorders (PGT-M) has been used to select genetic disease-free embryos for implantation during in vitro fertilization (IVF) treatment. However, embryos tested by PGT-M have risks of harboring chromosomal aneuploidy. Hence, a universal method to detect monogenic diseases and genomic imbalances is required. Methods: Here, we report a novel PGT-A/M procedure allowing simultaneous detection of monogenic diseases and genomic imbalances in one experiment. Library was prepared in a special way that multiplex polymerase chain reaction (PCR) was integrated into the process of whole genome amplification. The resulting library was used for one-step low-pass whole genome sequencing (WGS) and high-depth target enrichment sequencing (TES). Results: The TAGs-seq PGT-A/M was first validated with genomic DNA (gDNA) and the multiple displacement amplification (MDA) products of a cell line. Over 90% of sequencing reads covered the whole-genome region with around 0.3–0.4 × depth, while around 5.4%–7.3% of reads covered target genes with >10000 × depth. Then, for clinical validation, 54 embryos from 8 women receiving PGT-M of β-thalassemia were tested by the TAGs-seq PGT-A/M. In each embryo, an average of 20.0 million reads with 0.3 × depth of the whole-genome region was analyzed for genomic imbalance, while an average of 0.9 million reads with 11260.0 × depth of the target gene HBB were analyzed for β-thalassemia. Eventually, 18 embryos were identified with genomic imbalance with 81.1% consistency to karyomapping results. 10 embryos contained β-thalassemia with 100% consistency to conventional PGT-M method. Conclusion: TAGs-seq PGT-A/M simultaneously detected genomic imbalance and monogenic disease in embryos without dramatic increase of sequencing data output.
Collapse
Affiliation(s)
- Lin Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jun Xia
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Chenhui Ding
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | | | - Jiafu Pan
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanhong Zeng
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | | | - Yanwen Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| | - Canquan Zhou
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| |
Collapse
|
3
|
Hamdi Y, Boujemaa M, Mighri N, Mejri N, Jaidane O, Ben Nasr S, Bouaziz H, Hassouna JB, Zribi A, Berrazaga Y, Rachdi H, Daoud N, El Benna H, Labidi S, Haddaoui A, Rahal K, Benna F, Boussen H, Abdelhak S, Boubaker S. Identification of BRCA2 Cis Double Heterozygous Breast Cancer Cases Using Whole Exome Sequencing: Phenotypic Expression and Impact on Personalized Oncology. Front Genet 2021; 12:674990. [PMID: 34456966 PMCID: PMC8397457 DOI: 10.3389/fgene.2021.674990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/08/2021] [Indexed: 12/24/2022] Open
Abstract
BRCA1 and BRCA2 are the most commonly mutated breast cancer susceptibility genes that convey a high risk of breast and ovarian cancer. Most BRCA1 or BRCA2 mutation carriers have inherited a single heterozygous mutation. In recent years, very rare cases with biallelic or trans double heterozygous mutations on BRCA1 and or BRCA2 have been identified and seem to be associated with distinctive phenotypes. Given that this genotype-phenotype correlation in cancer predisposing hereditary conditions is of relevance for oncological prevention and genetic testing, it is important to investigate these rare BRCA genotypes for better clinical management of BRCA mutation carriers. Here we present the first report on Cis double heterozygosity (Cis DH) on BRCA2 gene identified using Whole exome sequencing (WES) in a Tunisian family with two BRCA2 mutations namely: c.632-1G>A and c.1310_1313DelAAGA that are both reported as pathogenic in ClinVar database. Subsequent analysis in 300 high-risk Tunisian breast cancer families detected this Cis double heterozygous genotype in 8 additional individuals belonging to 5 families from the same geographic origin suggesting a founder effect. Moreover, the observed Cis DH seems to be associated with an early age of onset (mean age = 35.33 years) and severe phenotype of the disease with high breast cancer grade and multiple cancer cases in the family. The identification of unusual BRCA genotypes in this Tunisian cohort highlights the importance of performing genetic studies in under-investigated populations. This will also potentially help avoiding erroneous classifications of genetic variants in African population and therefore avoiding clinical misdiagnosis of BRCA related cancers. Our findings will also have an impact on the genetic testing and the clinical management of North African breast cancer patients as well as patients from different other ethnic groups in regard to several emerging target therapies such as PARP inhibitors.
Collapse
Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Olfa Jaidane
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Sonia Ben Nasr
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Department of Medical Oncology, Military Hospital, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Jamel Ben Hassouna
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Aref Zribi
- Department of Medical Oncology, Military Hospital, Tunis, Tunisia
| | - Yossra Berrazaga
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Haifa Rachdi
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Nouha Daoud
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Houda El Benna
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | | | - Khaled Rahal
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Farouk Benna
- Department of Radiation Oncology, University of Tunis, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| |
Collapse
|
4
|
Sallevelt SCEH, Stegmann APA, de Koning B, Velter C, Steyls A, van Esch M, Lakeman P, Yntema H, Esteki MZ, de Die-Smulders CEM, Gilissen C, van den Wijngaard A, Brunner HG, Paulussen ADC. Diagnostic exome-based preconception carrier testing in consanguineous couples: results from the first 100 couples in clinical practice. Genet Med 2021; 23:1125-1136. [PMID: 33742171 PMCID: PMC8187149 DOI: 10.1038/s41436-021-01116-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 01/20/2023] Open
Abstract
Purpose Consanguineous couples are at increased risk of being heterozygous for the same autosomal recessive (AR) disorder(s), with a 25% risk of affected offspring as a consequence. Until recently, comprehensive preconception carrier testing (PCT) for AR disorders was unavailable in routine diagnostics. Here we developed and implemented such a test in routine clinical care. Methods We performed exome sequencing (ES) for 100 consanguineous couples. For each couple, rare variants that could give rise to biallelic variants in offspring were selected. These variants were subsequently filtered against a gene panel consisting of ~2,000 genes associated with known AR disorders (OMIM-based). Remaining variants were classified according to American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines, after which only likely pathogenic and pathogenic (class IV/V) variants, present in both partners, were reported. Results In 28 of 100 tested consanguineous couples (28%), likely pathogenic and pathogenic variants not previously known in the couple or their family were reported conferring 25% risk of affected offspring. Conclusion ES-based PCT provides a powerful diagnostic tool to identify AR disease carrier status in consanguineous couples. Outcomes provided significant reproductive choices for a higher proportion of these couples than previous tests.
Collapse
Affiliation(s)
- Suzanne C E H Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Crool Velter
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Anja Steyls
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Melanie van Esch
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Phillis Lakeman
- Amsterdam UMC, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Christine E M de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.,Donders center for Neuroscience, Radboudumc, Nijmegen, The Netherlands.,MHENS school of Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Aimée D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands. .,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.
| |
Collapse
|
5
|
Shaw T, Chan SH, Teo JX, Chong ST, Li ST, Courtney E, Ishak D, Sankar H, Ang ZLT, Chiang J, Loh M, Zhou L, Lee SC, Yeh HY, Kolinjivadi AM, Lim WK, Ngeow J. Investigation into the origins of an ancient BRCA1 founder mutation identified among Chinese families in Singapore. Int J Cancer 2020; 148:637-645. [PMID: 32745242 DOI: 10.1002/ijc.33241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 11/07/2022]
Abstract
Identification of ancestry-specific pathogenic variants is imperative for diagnostic, treatment, management and prevention strategies, and to understand penetrance/modifiers on risk. Our study aimed to determine the clinical significance of a recurrent BRCA1 c.442-22_442-13del variant of unknown significance identified among 13 carriers from six Chinese families, all with a significant history of breast and/or ovarian cancer. We further aimed to establish whether this was due to a founder effect and explore its origins. Haplotype analysis, using nine microsatellite markers encompassing 2.5 megabase pairs around the BRCA1 locus, identified a common haploblock specific to the variant carriers, confirming a founder effect. Variant age was estimated to date back 77.9 generations to 69 bc using the Gamma approach. On principal component analysis using single nucleotide polymorphisms merged with 1000 Genomes dataset, variant carriers were observed to overlap predominantly with the southern Han Chinese population. To determine pathogenicity of the variant, we assessed the functional effect on RAD51 foci formation as well as replication fork stability upon induction of DNA damage and observed an impaired DNA repair response associated with the variant. In summary, we identified an ancient Chinese founder mutation dating back 77.9 generations, possibly common among individuals of southern Han Chinese descent. Using evidence from phenotypic/family history studies, segregation analysis and functional characterization, the BRCA1 variant was reclassified from uncertain significance to pathogenic.
Collapse
Affiliation(s)
- Tarryn Shaw
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Siao Ting Chong
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Shao-Tzu Li
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Eliza Courtney
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Diana Ishak
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Haresh Sankar
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Zoe Li Ting Ang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Li Zhou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Hui-Yuan Yeh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| |
Collapse
|
6
|
Masset H, Zamani Esteki M, Dimitriadou E, Dreesen J, Debrock S, Derhaag J, Derks K, Destouni A, Drüsedau M, Meekels J, Melotte C, Peeraer K, Tšuiko O, van Uum C, Allemeersch J, Devogelaere B, François KO, Happe S, Lorson D, Richards RL, Theuns J, Brunner H, de Die-Smulders C, Voet T, Paulussen A, Coonen E, Vermeesch JR. Multi-centre evaluation of a comprehensive preimplantation genetic test through haplotyping-by-sequencing. Hum Reprod 2020; 34:1608-1619. [PMID: 31348829 DOI: 10.1093/humrep/dez106] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/16/2019] [Indexed: 12/14/2022] Open
Abstract
STUDY QUESTION Can reduced representation genome sequencing offer an alternative to single nucleotide polymorphism (SNP) arrays as a generic and genome-wide approach for comprehensive preimplantation genetic testing for monogenic disorders (PGT-M), aneuploidy (PGT-A) and structural rearrangements (PGT-SR) in human embryo biopsy samples? SUMMARY ANSWER Reduced representation genome sequencing, with OnePGT, offers a generic, next-generation sequencing-based approach for automated haplotyping and copy-number assessment, both combined or independently, in human single blastomere and trophectoderm samples. WHAT IS KNOWN ALREADY Genome-wide haplotyping strategies, such as karyomapping and haplarithmisis, have paved the way for comprehensive PGT, i.e. leveraging PGT-M, PGT-A and PGT-SR in a single workflow. These methods are based upon SNP array technology. STUDY DESIGN, SIZE, DURATION This multi-centre verification study evaluated the concordance of PGT results for a total of 225 embryos, including 189 originally tested for a monogenic disorder and 36 tested for a translocation. Concordance for whole chromosome aneuploidies was also evaluated where whole genome copy-number reference data were available. Data analysts were kept blind to the results from the reference PGT method. PARTICIPANTS/MATERIALS, SETTING, METHODS Leftover blastomere/trophectoderm whole genome amplified (WGA) material was used, or secondary trophectoderm biopsies were WGA. A reduced representation library from WGA DNA together with bulk DNA from phasing references was processed across two study sites with the Agilent OnePGT solution. Libraries were sequenced on an Illumina NextSeq500 system, and data were analysed with Agilent Alissa OnePGT software. The embedded PGT-M pipeline utilises the principles of haplarithmisis to deduce haplotype inheritance whereas both the PGT-A and PGT-SR pipelines are based upon read-count analysis in order to evaluate embryonic ploidy. Concordance analysis was performed for both analysis strategies against the reference PGT method. MAIN RESULTS AND THE ROLE OF CHANCE PGT-M analysis was performed on 189 samples. For nine samples, the data quality was too poor to analyse further, and for 20 samples, no result could be obtained mainly due to biological limitations of the haplotyping approach, such as co-localisation of meiotic crossover events and nullisomy for the chromosome of interest. For the remaining 160 samples, 100% concordance was obtained between OnePGT and the reference PGT-M method. Equally for PGT-SR, 100% concordance for all 36 embryos tested was demonstrated. Moreover, with embryos originally analysed for PGT-M or PGT-SR for which genome-wide copy-number reference data were available, 100% concordance was shown for whole chromosome copy-number calls (PGT-A). LIMITATIONS, REASONS FOR CAUTION Inherent to haplotyping methodologies, processing of additional family members is still required. Biological limitations caused inconclusive results in 10% of cases. WIDER IMPLICATIONS OF THE FINDINGS Employment of OnePGT for PGT-M, PGT-SR, PGT-A or combined as comprehensive PGT offers a scalable platform, which is inherently generic and thereby, eliminates the need for family-specific design and optimisation. It can be considered as both an improvement and complement to the current methodologies for PGT. STUDY FUNDING/COMPETING INTEREST(S) Agilent Technologies, the KU Leuven (C1/018 to J.R.V. and T.V.) and the Horizon 2020 WIDENLIFE (692065 to J.R.V. and T.V). H.M. is supported by the Research Foundation Flanders (FWO, 11A7119N). M.Z.E, J.R.V. and T.V. are co-inventors on patent applications: ZL910050-PCT/EP2011/060211- WO/2011/157846 'Methods for haplotyping single cells' and ZL913096-PCT/EP2014/068315 'Haplotyping and copy-number typing using polymorphic variant allelic frequencies'. T.V. and J.R.V. are co-inventors on patent application: ZL912076-PCT/EP2013/070858 'High-throughput genotyping by sequencing'. Haplarithmisis ('Haplotyping and copy-number typing using polymorphic variant allelic frequencies') has been licensed to Agilent Technologies. The following patents are pending for OnePGT: US2016275239, AU2014345516, CA2928013, CN105874081, EP3066213 and WO2015067796. OnePGT is a registered trademark. D.L., J.T. and R.L.R. report personal fees during the conduct of the study and outside the submitted work from Agilent Technologies. S.H. and K.O.F. report personal fees and other during the conduct of the study and outside the submitted work from Agilent Technologies. J.A. reports personal fees and other during the conduct of the study from Agilent Technologies and personal fees from Agilent Technologies and UZ Leuven outside the submitted work. B.D. reports grants from IWT/VLAIO, personal fees during the conduct of the study from Agilent Technologies and personal fees and other outside the submitted work from Agilent Technologies. In addition, B.D. has a patent 20160275239 - Genetic Analysis Method pending. The remaining authors have no conflicts of interest.
Collapse
Affiliation(s)
- Heleen Masset
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Masoud Zamani Esteki
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | | | - Jos Dreesen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Sophie Debrock
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Josien Derhaag
- Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands.,Department of Obstetrics and Gynaecology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Kasper Derks
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Aspasia Destouni
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, USA
| | - Marion Drüsedau
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jeroen Meekels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Cindy Melotte
- Center for Human Genetics, University Hospitals of Leuven, Leuven, Belgium
| | - Karen Peeraer
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Olga Tšuiko
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chris van Uum
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Joke Allemeersch
- Diagnostics and Genomics Group, Agilent Technologies, Heverlee, Belgium
| | | | | | - Scott Happe
- Diagnostics and Genomics Group, Agilent Technologies, Cedar Creek, TX, USA
| | - Dennis Lorson
- Diagnostics and Genomics Group, Agilent Technologies, Heverlee, Belgium
| | - Rebecca Louise Richards
- Diagnostics and Genomics Group, Agilent Technologies, Heverlee, Belgium.,Diagnostics and Genomics Group, Agilent Technologies, Niel, Belgium
| | - Jessie Theuns
- Diagnostics and Genomics Group, Agilent Technologies, Niel, Belgium
| | - Han Brunner
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Christine de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Aimée Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Edith Coonen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Joris Robert Vermeesch
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Center for Human Genetics, University Hospitals of Leuven, Leuven, Belgium
| |
Collapse
|
7
|
Zhang X, Niu J, Che T, Zhu Y, Zhang H, Qu J. Fertility preservation in BRCA mutation carriers-efficacy and safety issues: a review. Reprod Biol Endocrinol 2020; 18:11. [PMID: 32070378 PMCID: PMC7027288 DOI: 10.1186/s12958-019-0561-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/27/2019] [Indexed: 02/08/2023] Open
Abstract
BRCA mutation carriers face various situations that influence their fertility potential. There is still a lack of guideline or expert consensus on Fertility Preservation (FP) in BRCA mutation carriers and the necessity and safety of FP in BRCA mutation carriers is still in dispute. This review aims to focus on the population of BRCA mutation carriers by analyzing the existing FP strategies, comprehensively comparing the pros and cons of each strategy and its applicability.FP is a suggestion for BRCA mutation carriers with birth planning. Different FP strategies have different characteristics. Considering the particularity of BRCA mutation carriers, multiple factors need to be carefully considered. This review focuses on the applicability of each FP method for carriers under various circumstances. Available FP strategies including oocyte cryopreservation, ovarian tissue cryopreservation, preimplantation genetic diagnosis, and egg/embryo donation are analyzed by comparing existing methods comprehensively. In the attempt to provide an up-to-date decision-making guidance. Conditions taking into consideration were the carrier's age, the risk of breast and ovarian metastasis, plans for oncotherapy, FP outcome, time available for FP intervention and accessibility.Overall, FP is necessary and safe for BRCA mutation carriers. Among all available FP methods, oocyte cryopreservation is the most reliable procedure; ovarian tissue cryopreservation is the only way for preserving both fertility and endocrine function, recommended for pre-pubertal carriers and when time is limited for oocyte stimulation. A clear framework provides frontline clinical practitioners a new thought and eventually benefit thousands of BRCA mutation carriers.
Collapse
Affiliation(s)
- Xiaofu Zhang
- Department of Clinical Medicine, Medical College of Soochow University, Ren Ai Road 199, Suzhou Industrial Park, Suzhou, 215123, China
| | - Jingxin Niu
- Department of Clinical Medicine, Medical College of Soochow University, Ren Ai Road 199, Suzhou Industrial Park, Suzhou, 215123, China
| | - Tuanjie Che
- Laboratory of Precision Medicine and Translational Medicine, Suzhou Hospital Affiliated to Nanjing Medical University, Suzhou Science and Technology Town Hospital, Suzhou, 215153, China
| | - Yibei Zhu
- Department of Immunology, Medical College of Soochow University, Ren Ai Road 199, Suzhou Industrial Park, Suzhou, 215123, China
| | - Hongtao Zhang
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China
| | - Jing Qu
- Department of Cell Biology, Medical College of Soochow University, Ren Ai Road 199, Suzhou Industrial Park, Suzhou, 215123, China.
| |
Collapse
|
8
|
Derks-Smeets IAP, Schrijver LH, de Die-Smulders CEM, Tjan-Heijnen VCG, van Golde RJT, Smits LJ, Caanen B, van Asperen CJ, Ausems M, Collée M, van Engelen K, Kets CM, van der Kolk L, Oosterwijk JC, van Os TAM, Rookus MA, van Leeuwen FE, Gómez García EB. Ovarian stimulation for IVF and risk of primary breast cancer in BRCA1/2 mutation carriers. Br J Cancer 2018; 119:357-363. [PMID: 29937543 PMCID: PMC6068188 DOI: 10.1038/s41416-018-0139-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 04/23/2018] [Accepted: 05/14/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The effect of in vitro fertilisation (IVF) on breast cancer risk for BRCA1/2 mutation carriers is rarely examined. As carriers may increasingly undergo IVF as part of preimplantation genetic diagnosis (PGD), we examined the impact of ovarian stimulation for IVF on breast cancer risk in BRCA1/2 mutation carriers. METHODS The study population consisted of 1550 BRCA1 and 964 BRCA2 mutation carriers, derived from the nationwide HEBON study and the nationwide PGD registry. Questionnaires, clinical records and linkages with the Netherlands Cancer Registry were used to collect data on IVF exposure, risk-reducing surgeries and cancer diagnosis, respectively. Time-dependent Cox regression analyses were conducted, stratified for birth cohort and adjusted for subfertility. RESULTS Of the 2514 BRCA1/2 mutation carriers, 3% (n = 76) were exposed to ovarian stimulation for IVF. In total, 938 BRCA1/2 mutation carriers (37.3%) were diagnosed with breast cancer. IVF exposure was not associated with risk of breast cancer (HR: 0.79, 95% CI: 0.46-1.36). Similar results were found for the subgroups of subfertile women (n = 232; HR: 0.73, 95% CI: 0.39-1.37) and BRCA1 mutation carriers (HR: 1.12, 95% CI: 0.60-2.09). In addition, age at and recency of first IVF treatment were not associated with breast cancer risk. CONCLUSION No evidence was found for an association between ovarian stimulation for IVF and breast cancer risk in BRCA1/2 mutation carriers.
Collapse
Affiliation(s)
- Inge A P Derks-Smeets
- Department of Clinical Genetics, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Lieske H Schrijver
- Department of Epidemiology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Christine E M de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Vivianne C G Tjan-Heijnen
- GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Ron J T van Golde
- GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Obstetrics and Gynaecology, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Luc J Smits
- Department of Epidemiology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Beppy Caanen
- Department of Clinical Genetics, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre Leiden, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Margreet Ausems
- Department of Genetics, University Medical Centre Utrecht, P.O. 85500, 3508 GA, Utrecht, The Netherlands
| | - Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Klaartje van Engelen
- Department of Clinical Genetics, VU University Medical Centre, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - C Marleen Kets
- Department of Human Genetics, Radboud University Medical Centre, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Lizet van der Kolk
- Family Cancer Clinic, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jan C Oosterwijk
- Department of Genetics, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - Theo A M van Os
- Department of Clinical Genetics, Academic Medical Centre, P.O. Box 22700, 1100 DE, Amsterdam, The Netherlands
| | | | - Matti A Rookus
- Department of Epidemiology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Flora E van Leeuwen
- Department of Epidemiology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.
| | - Encarna B Gómez García
- Department of Clinical Genetics, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| |
Collapse
|
9
|
Hao Y, Chen D, Zhang Z, Zhou P, Cao Y, Wei Z, Xu X, Chen B, Zou W, Lv M, Ji D, He X. Successful preimplantation genetic diagnosis by targeted next-generation sequencing on an ion torrent personal genome machine platform. Oncol Lett 2018. [PMID: 29541197 PMCID: PMC5835955 DOI: 10.3892/ol.2018.7876] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Hearing loss may place a heavy burden on the patient and patient's family. Given the high incidence of hearing loss among newborns and the huge cost of treatment and care (including cochlear implantation), prenatal diagnosis is strongly recommended. Termination of the fetus may be considered as an extreme outcome to the discovery of a potential deaf fetus, and therefore preimplantation genetic diagnosis has become an important option for avoiding the birth of affected children without facing the risk of abortion following prenatal diagnosis. In one case, a couple had a 7-year-old daughter affected by non-syndromic sensorineural hearing loss. The affected fetus carried a causative compound heterozygous mutation c.919-2 A>G (IVS7-2 A>G) and c.1707+5 G>A (IVS15+5 G>A) of the solute carrier family 26 member 4 gene inherited from maternal and paternal sides, respectively. The present study applied multiple displacement amplification for whole genome amplification of biopsied trophectoderm cells and next-generation sequencing (NGS)-based single nucleotide polymorphism haplotyping on an Ion Torrent Personal Genome Machine. One unaffected embryo was transferred in a frozen-thawed embryo transfer cycle and the patient was impregnated. To conclude, to the best of our knowledge, this may be the first report of NGS-based preimplantation genetic diagnosis (PGD) for non-syndromic hearing loss caused by a compound heterozygous mutation using an Ion Torrent Personal Genome Machine. NGS provides unprecedented high-throughput, highly parallel and base-pair resolution data for genetic analysis. The method meets the requirements of medium-sized diagnostics laboratories. With decreased costs compared with previous techniques (such as Sanger sequencing), this technique may have potential widespread clinical application in PGD of other types of monogenic disease.
Collapse
Affiliation(s)
- Yan Hao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Dawei Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Zhiguo Zhang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Ping Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Zhaolian Wei
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xiaofeng Xu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Beili Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Weiwei Zou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Mingrong Lv
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Dongmei Ji
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xiaojin He
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| |
Collapse
|
10
|
Derks-Smeets IAP, van Tilborg TC, van Montfoort A, Smits L, Torrance HL, Meijer-Hoogeveen M, Broekmans F, Dreesen JCFM, Paulussen ADC, Tjan-Heijnen VCG, Homminga I, van den Berg MMJ, Ausems MGEM, de Rycke M, de Die-Smulders CEM, Verpoest W, van Golde R. BRCA1 mutation carriers have a lower number of mature oocytes after ovarian stimulation for IVF/PGD. J Assist Reprod Genet 2017; 34:1475-1482. [PMID: 28831696 PMCID: PMC5699993 DOI: 10.1007/s10815-017-1014-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/28/2017] [Indexed: 01/07/2023] Open
Abstract
Purpose The aim of this study was to determine whether BRCA1/2 mutation carriers produce fewer mature oocytes after ovarian stimulation for in vitro fertilization (IVF) with preimplantation genetic diagnosis (PGD), in comparison to a PGD control group. Methods A retrospective, international, multicenter cohort study was performed on data of first PGD cycles performed between January 2006 and September 2015. Data were extracted from medical files. The study was performed in one PGD center and three affiliated IVF centers in the Netherlands and one PGD center in Belgium. Exposed couples underwent PGD because of a pathogenic BRCA1/2 mutation, controls for other monogenic conditions. Only couples treated in a long gonadotropin-releasing hormone (GnRH) agonist-suppressive protocol, stimulated with at least 150 IU follicle stimulating hormone (FSH), were included. Women suspected to have a diminished ovarian reserve status due to chemotherapy, auto-immune disorders, or genetic conditions (other than BRCA1/2 mutations) were excluded. A total of 106 BRCA1/2 mutation carriers underwent PGD in this period, of which 43 (20 BRCA1 and 23 BRCA2 mutation carriers) met the inclusion criteria. They were compared to 174 controls selected by frequency matching. Results Thirty-eight BRCA1/2 mutation carriers (18 BRCA1 and 20 BRCA2 mutation carriers) and 154 controls proceeded to oocyte pickup. The median number of mature oocytes was 7.0 (interquartile range (IQR) 4.0–9.0) in the BRCA group as a whole, 6.5 (IQR 4.0–8.0) in BRCA1 mutation carriers, 7.5 (IQR 5.5–9.0) in BRCA2 mutation carriers, and 8.0 (IQR 6.0–11.0) in controls. Multiple linear regression analysis with the number of mature oocytes as a dependent variable and adjustment for treatment center, female age, female body mass index (BMI), type of gonadotropin used, and the total dose of gonadotropins administered revealed a significantly lower yield of mature oocytes in the BRCA group as compared to controls (p = 0.04). This finding could be fully accounted for by the BRCA1 subgroup (BRCA1 mutation carriers versus controls p = 0.02, BRCA2 mutation carriers versus controls p = 0.50). Conclusions Ovarian response to stimulation, expressed as the number of mature oocytes, was reduced in BRCA1 but not in BRCA2 mutation carriers. Although oocyte yield was in correspondence to a normal response in all subgroups, this finding points to a possible negative influence of the BRCA1 gene on ovarian reserve. Electronic supplementary material The online version of this article (doi:10.1007/s10815-017-1014-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- I A P Derks-Smeets
- Department of Clinical Genetics, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - T C van Tilborg
- Department of Reproductive Medicine, University Medical Center Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - A van Montfoort
- GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Obstetrics and Gynecology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - L Smits
- Department of Epidemiology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - H L Torrance
- Department of Reproductive Medicine, University Medical Center Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - M Meijer-Hoogeveen
- Department of Reproductive Medicine, University Medical Center Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - F Broekmans
- Department of Reproductive Medicine, University Medical Center Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - J C F M Dreesen
- Department of Clinical Genetics, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - A D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - V C G Tjan-Heijnen
- GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - I Homminga
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - M M J van den Berg
- Center for Reproductive Medicine, Academic Medical Center, P.O. Box 22660, 1100 DD, Amsterdam, The Netherlands
| | - M G E M Ausems
- Department of Genetics, University Medical Center Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - M de Rycke
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090, Brussels, Belgium
| | - C E M de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - W Verpoest
- Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090, Brussels, Belgium
| | - R van Golde
- GROW - School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands. .,Department of Obstetrics and Gynecology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
| |
Collapse
|
11
|
Kamps R, Brandão RD, Bosch BJVD, Paulussen ADC, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci 2017; 18:ijms18020308. [PMID: 28146134 PMCID: PMC5343844 DOI: 10.3390/ijms18020308] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.
Collapse
Affiliation(s)
- Rick Kamps
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Rita D Brandão
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Bianca J van den Bosch
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Aimee D C Paulussen
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Sofia Xanthoulea
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Marinus J Blok
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| |
Collapse
|
12
|
Präimplantationsdiagnostik – methodische Aspekte. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0103-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Zusammenfassung
Die Präimplantationsdiagnostik erfordert eine enge und vertrauensvolle interdisziplinäre Zusammenarbeit zwischen hoch qualifizierten Fachärzten und Naturwissenschaftlern aus Humangenetik und Reproduktionsmedizin. In einem sehr engen Zeitfenster müssen komplexe Laborabläufe standardisiert und qualitätsgesichert umgesetzt werden. In diesem Beitrag sollen orientierende Empfehlungen zur Umsetzung kurz vorgestellt werden. Zentral haben wir häufigere Problemsituationen thematisiert, welche bereits bei der Indikationsstellung wie auch bei den nachfolgenden Schritten in der genetischen Analyse, Datenauswertung und Befunderstellung mögliche Fehlerquellen darstellen. Ziel unserer verantwortlichen Arbeit an den PID-Zentren sollte eine hohe Geburtenrate bei hoher Diagnosesicherheit mit möglichst wenigen schonenden Behandlungszyklen sein.
Collapse
|
13
|
|
14
|
Chandrasekharan S, McGuire AL, Van den Veyver IB. Do recent US Supreme Court rulings on patenting of genes and genetic diagnostics affect the practice of genetic screening and diagnosis in prenatal and reproductive care? Prenat Diagn 2014; 34:921-6. [PMID: 24989832 PMCID: PMC4293120 DOI: 10.1002/pd.4445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 11/08/2022]
Abstract
Thousands of patents have been awarded that claim human gene sequences and their uses, and some have been challenged in court. In a recent high-profile case, Association for Molecular Pathology, et al. v. Myriad Genetics, Inc., et al., the US Supreme Court ruled that genes are natural occurring substances and therefore not patentable through 'composition of matter' claims. The consequences of this ruling will extend well beyond ending Myriad's monopoly over BRCA testing and may affect similar monopolies of other commercial laboratories for tests involving other genes. It could also simplify intellectual property issues surrounding genome-wide clinical sequencing, which can generate results for genes covered by intellectual property. Non-invasive prenatal testing (NIPT) for common aneuploidies using cell-free fetal (cff) DNA in maternal blood is currently offered through commercial laboratories and is also the subject of ongoing patent litigation. The recent Supreme Court decision in the Myriad case has already been invoked by a lower district court in NIPT litigation and resulted in invalidation of primary claims in a patent on currently marketed cffDNA-based testing for chromosomal aneuploidies.
Collapse
Affiliation(s)
- Subhashini Chandrasekharan
- Science and Society Initiative, Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA
| | - Amy L. McGuire
- Department of Medicine and Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston TX, USA
| | - Ignatia B. Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, USA
| |
Collapse
|
15
|
Yan L, Wei Y, Huang J, Zhu X, Shi X, Xia X, Yan J, Lu C, Lian Y, Li R, Liu P, Qiao J. Advances in preimplantation genetic diagnosis/screening. SCIENCE CHINA-LIFE SCIENCES 2014; 57:665-71. [PMID: 24907939 DOI: 10.1007/s11427-014-4683-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 04/28/2014] [Indexed: 11/30/2022]
Affiliation(s)
- LiYing Yan
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Genome-wide karyomapping accurately identifies the inheritance of single-gene defects in human preimplantation embryos in vitro. Genet Med 2014; 16:838-45. [PMID: 24810687 PMCID: PMC4225458 DOI: 10.1038/gim.2014.45] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/31/2014] [Indexed: 11/21/2022] Open
Abstract
Purpose: Our aim was to compare the accuracy of family- or disease-specific targeted haplotyping and direct mutation-detection strategies with the accuracy of genome-wide mapping of the parental origin of each chromosome, or karyomapping, by single-nucleotide polymorphism genotyping of the parents, a close relative of known disease status, and the embryo cell(s) used for preimplantation genetic diagnosis of single-gene defects in a single cell or small numbers of cells biopsied from human embryos following in vitro fertilization. Methods: Genomic DNA and whole-genome amplification products from embryo samples, which were previously diagnosed by targeted haplotyping, were genotyped for single-nucleotide polymorphisms genome-wide detection and retrospectively analyzed blind by karyomapping. Results: Single-nucleotide polymorphism genotyping and karyomapping were successful in 213/218 (97.7%) samples from 44 preimplantation genetic diagnosis cycles for 25 single-gene defects with various modes of inheritance distributed widely across the genome. Karyomapping was concordant with targeted haplotyping in 208 (97.7%) samples, and the five nonconcordant samples were all in consanguineous regions with limited or inconsistent haplotyping results. Conclusion: Genome-wide karyomapping is highly accurate and facilitates analysis of the inheritance of almost any single-gene defect, or any combination of loci, at the single-cell level, greatly expanding the range of conditions for which preimplantation genetic diagnosis can be offered clinically without the need for customized test development.
Collapse
|
17
|
Derks-Smeets IAP, de Die-Smulders CEM, Mackens S, van Golde R, Paulussen AD, Dreesen J, Tournaye H, Verdyck P, Tjan-Heijnen VCG, Meijer-Hoogeveen M, De Greve J, Geraedts J, De Rycke M, Bonduelle M, Verpoest WM. Hereditary breast and ovarian cancer and reproduction: an observational study on the suitability of preimplantation genetic diagnosis for both asymptomatic carriers and breast cancer survivors. Breast Cancer Res Treat 2014; 145:673-81. [DOI: 10.1007/s10549-014-2951-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 11/28/2022]
|