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Exome sequencing reveals pathogenic variants in known and novel candidate genes for severe sperm motility disorders.

The dataset is composed by the raw and processed sequencing data generated from 8 Australian Patients and 13 Argentinian Patients affected by a form of male infertility characterised by vital, but immotile sperm often in combination with a spectrum of structural abnormalities of the sperm flagellum.

Request Access

The Newcastle University Male Infertility Genomics DAC requests that any person or group wishing to gain access to the genomic data related to this study must sign the Data Access Policy before being allowed to access the genomic data of these patients.

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom the Newcastle University Male Infertility Genomics DAC grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The Newcastle University Male Infertility Genomics DAC and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. Newcastle University Male Infertility Genomics DAC: Data access committee for the Male Infertility Genomics research group lead by Professor Joris Veltman at Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, United Kingdom. 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines ( ) and the Toronto Statement ( This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) ( ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) ( ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify the Newcastle University Male Infertility Genomics DAC within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the Newcastle University Male Infertility Genomics DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the Newcastle University Male Infertility Genomics DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Newcastle University Male Infertility Genomics DAC may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than the Newcastle University Male Infertility Genomics DAC. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of England and Wales and shall be subject to the exclusive jurisdiction of the English courts. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for the Newcastle University Male Infertility Genomics DAC Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) EGA Study ID: EGAS00001005018 Dataset details: The dataset is composed by the raw and processed sequencing data generated from 8 Australian Patients and 13 Argentinian Patients affected by a form of male infertility characterised by vital, but immotile sperm often in combination with a spectrum of structural abnormalities of the sperm flagellum. Name of project that created the dataset Exome sequencing reveals pathogenic variants in known and novel candidate genes for severe sperm motility disorders. Names of other data producers/collaborators Moira K. O’Bryan - School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, Australia Hector Edgardo Chemes - Center for Research in Endocrinology, Buenos Aires Children’s Hospital, Buenos Aires, Argentina Specific limitations on areas of research The dataset should only be used for purposes of genetic studies in the field of infertility and is not adequate for other areas of research unless an adequate rational is provided. Minimum protection measures required The identity and anonymity of the subjects must be ensured at all times and findings relating to the health and wellbeing of these individuals should not be divulged without obtaining previous consent from them and the Newcastle University Male Infertility Genomics DAC. File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY The Newcastle University Male Infertility Genomics DAC intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. The Newcastle University Male Infertility Genomics DAC anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 6 months after these data were first made available on the relevant hosting database, unless the Newcastle University Male Infertility Genomics DAC has provided written consent to earlier submission. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with the Newcastle University Male Infertility Genomics DAC.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001005018 Other
ID File Type Size Located in
EGAF00004996083 fastq.gz 1.2 GB
EGAF00004996084 fastq.gz 1.2 GB
EGAF00004996085 fastq.gz 1.2 GB
EGAF00004996086 fastq.gz 1.2 GB
EGAF00004996087 fastq.gz 1.2 GB
EGAF00004996088 fastq.gz 1.2 GB
EGAF00004996089 fastq.gz 1.2 GB
EGAF00004996090 fastq.gz 1.2 GB
EGAF00004996109 fastq.gz 1.7 GB
EGAF00004996110 fastq.gz 1.7 GB
EGAF00004996111 fastq.gz 1.8 GB
EGAF00004996112 fastq.gz 1.8 GB
EGAF00004996113 fastq.gz 1.8 GB
EGAF00004996114 fastq.gz 1.8 GB
EGAF00004996115 fastq.gz 1.2 GB
EGAF00004996116 fastq.gz 1.2 GB
EGAF00004996117 fastq.gz 1.7 GB
EGAF00004996118 fastq.gz 1.7 GB
EGAF00004996119 fastq.gz 1.2 GB
EGAF00004996120 fastq.gz 1.2 GB
EGAF00004996121 fastq.gz 1.2 GB
EGAF00004996122 fastq.gz 1.2 GB
EGAF00004996123 fastq.gz 1.2 GB
EGAF00004996124 fastq.gz 1.2 GB
EGAF00004996133 fastq.gz 1.3 GB
EGAF00004996134 fastq.gz 1.4 GB
EGAF00004996135 fastq.gz 1.3 GB
EGAF00004996136 fastq.gz 1.3 GB
EGAF00004996137 fastq.gz 1.4 GB
EGAF00004996138 fastq.gz 1.4 GB
EGAF00004996139 fastq.gz 1.4 GB
EGAF00004996140 fastq.gz 1.4 GB
EGAF00004996146 bam 20.0 GB
EGAF00004996147 bai 4.2 MB
EGAF00004996162 fastq.gz 1.1 GB
EGAF00004996163 fastq.gz 1.1 GB
EGAF00004996164 fastq.gz 1.1 GB
EGAF00004996165 fastq.gz 1.1 GB
EGAF00004996166 fastq.gz 1.2 GB
EGAF00004996167 fastq.gz 1.2 GB
EGAF00004996168 fastq.gz 1.1 GB
EGAF00004996169 fastq.gz 1.2 GB
EGAF00004996170 fastq.gz 1.2 GB
EGAF00004996171 fastq.gz 1.2 GB
EGAF00004996172 fastq.gz 1.2 GB
EGAF00004996173 fastq.gz 1.2 GB
EGAF00004996174 fastq.gz 1.2 GB
EGAF00004996175 fastq.gz 1.2 GB
EGAF00004996176 fastq.gz 1.2 GB
EGAF00004996177 fastq.gz 1.2 GB
EGAF00004996198 fastq.gz 1.3 GB
EGAF00004996199 fastq.gz 1.4 GB
EGAF00004996200 fastq.gz 1.3 GB
EGAF00004996201 fastq.gz 1.3 GB
EGAF00004996202 fastq.gz 1.4 GB
EGAF00004996203 fastq.gz 1.4 GB
EGAF00004996204 fastq.gz 1.1 GB
EGAF00004996205 fastq.gz 1.1 GB
EGAF00004996206 fastq.gz 1.1 GB
EGAF00004996207 fastq.gz 1.1 GB
EGAF00004996208 fastq.gz 1.2 GB
EGAF00004996209 fastq.gz 1.2 GB
EGAF00004996210 fastq.gz 1.2 GB
EGAF00004996211 fastq.gz 1.2 GB
EGAF00004996212 fastq.gz 1.4 GB
EGAF00004996213 fastq.gz 1.4 GB
EGAF00004996214 fastq.gz 1.2 GB
EGAF00004996215 fastq.gz 1.2 GB
EGAF00004996216 fastq.gz 1.2 GB
EGAF00004996217 fastq.gz 1.2 GB
EGAF00004996218 fastq.gz 1.2 GB
EGAF00004996219 fastq.gz 1.2 GB
EGAF00004996220 fastq.gz 1.2 GB
EGAF00004996221 fastq.gz 1.2 GB
EGAF00004996222 bam 30.5 GB
EGAF00004996223 bai 4.4 MB
EGAF00004999994 fastq.gz 1.2 GB
EGAF00004999995 fastq.gz 1.2 GB
EGAF00004999996 fastq.gz 1.1 GB
EGAF00004999997 fastq.gz 1.2 GB
EGAF00004999998 fastq.gz 1.2 GB
EGAF00004999999 fastq.gz 1.3 GB
EGAF00005000000 fastq.gz 1.1 GB
EGAF00005000001 fastq.gz 1.1 GB
EGAF00005000002 fastq.gz 1.3 GB
EGAF00005000003 fastq.gz 1.4 GB
EGAF00005000004 fastq.gz 1.2 GB
EGAF00005000005 fastq.gz 1.3 GB
EGAF00005000006 fastq.gz 1.5 GB
EGAF00005000007 fastq.gz 1.6 GB
EGAF00005000008 fastq.gz 1.4 GB
EGAF00005000009 fastq.gz 1.4 GB
EGAF00005000010 fastq.gz 1.2 GB
EGAF00005000011 fastq.gz 1.2 GB
EGAF00005000012 fastq.gz 1.4 GB
EGAF00005000013 fastq.gz 1.4 GB
EGAF00005000014 fastq.gz 1.4 GB
EGAF00005000015 fastq.gz 1.4 GB
EGAF00005000016 fastq.gz 1.3 GB
EGAF00005000017 fastq.gz 1.3 GB
EGAF00005000018 fastq.gz 1.5 GB
EGAF00005000019 fastq.gz 1.6 GB
EGAF00005000020 fastq.gz 1.4 GB
EGAF00005000021 fastq.gz 1.5 GB
EGAF00005000022 fastq.gz 1.3 GB
EGAF00005000023 fastq.gz 1.3 GB
EGAF00005000024 fastq.gz 1.2 GB
EGAF00005000025 fastq.gz 1.2 GB
EGAF00005000026 fastq.gz 1.6 GB
EGAF00005000027 fastq.gz 1.6 GB
EGAF00005000028 fastq.gz 1.5 GB
EGAF00005000029 fastq.gz 1.5 GB
EGAF00005000030 fastq.gz 1.5 GB
EGAF00005000031 fastq.gz 1.6 GB
EGAF00005000032 fastq.gz 1.4 GB
EGAF00005000033 fastq.gz 1.4 GB
EGAF00005000034 fastq.gz 1.4 GB
EGAF00005000035 fastq.gz 1.4 GB
EGAF00005000036 fastq.gz 1.3 GB
EGAF00005000037 fastq.gz 1.3 GB
EGAF00005000038 fastq.gz 1.7 GB
EGAF00005000039 fastq.gz 1.7 GB
EGAF00005000040 fastq.gz 1.6 GB
EGAF00005000041 fastq.gz 1.6 GB
EGAF00005000055 bam 20.1 GB
EGAF00005000056 bai 4.3 MB
EGAF00005000057 bam 23.0 GB
EGAF00005000058 bai 4.2 MB
EGAF00005000059 bam 19.2 GB
EGAF00005000060 bai 4.1 MB
EGAF00005000061 bam 20.0 GB
EGAF00005000062 bai 4.1 MB
EGAF00005000063 bam 24.7 GB
EGAF00005000064 bai 4.3 MB
EGAF00005000065 bam 20.3 GB
EGAF00005000066 bai 4.2 MB
EGAF00005000067 bam 21.4 GB
EGAF00005000068 bai 4.2 MB
EGAF00005000069 bam 10.5 GB
EGAF00005000070 bai 3.7 MB
EGAF00005000071 bam 10.8 GB
EGAF00005000072 bai 3.8 MB
EGAF00005000073 bam 11.9 GB
EGAF00005000074 bai 3.8 MB
EGAF00005000075 bam 12.5 GB
EGAF00005000076 bai 3.8 MB
EGAF00005000077 bam 11.7 GB
EGAF00005000078 bai 3.8 MB
EGAF00005000079 bam 12.2 GB
EGAF00005000080 bai 3.8 MB
EGAF00005000081 bam 13.7 GB
EGAF00005000082 bai 3.9 MB
EGAF00005000083 bam 11.7 GB
EGAF00005000084 bai 3.8 MB
EGAF00005000085 bam 14.2 GB
EGAF00005000086 bai 4.0 MB
EGAF00005000087 bam 13.3 GB
EGAF00005000088 bai 3.9 MB
EGAF00005000089 bam 12.2 GB
EGAF00005000090 bai 3.8 MB
EGAF00005000091 bam 16.2 GB
EGAF00005000092 bai 4.2 MB
EGAF00005000617 vcf 16.3 MB
EGAF00005000618 idx 1.2 MB
EGAF00005000619 vcf 21.8 MB
EGAF00005000620 idx 1.9 MB
EGAF00005000621 vcf 11.8 MB
EGAF00005000622 idx 1.4 MB
EGAF00005000623 vcf 15.6 MB
EGAF00005000624 idx 1.6 MB
EGAF00005000625 vcf 15.8 MB
EGAF00005000626 idx 1.5 MB
EGAF00005000627 vcf 18.3 MB
EGAF00005000628 idx 1.6 MB
EGAF00005000629 vcf 13.5 MB
EGAF00005000630 idx 1.0 MB
EGAF00005000631 vcf 13.9 MB
EGAF00005000632 idx 1.4 MB
EGAF00005000633 vcf 14.0 MB
EGAF00005000634 idx 787.3 kB
EGAF00005002427 vcf 20.1 MB
EGAF00005002428 idx 2.9 MB
EGAF00005002429 vcf 20.5 MB
EGAF00005002430 idx 2.8 MB
EGAF00005002431 vcf 21.7 MB
EGAF00005002432 idx 2.9 MB
EGAF00005002433 vcf 22.1 MB
EGAF00005002434 idx 2.7 MB
EGAF00005002435 vcf 21.1 MB
EGAF00005002436 idx 2.6 MB
EGAF00005002437 vcf 21.7 MB
EGAF00005002438 idx 2.7 MB
EGAF00005002439 vcf 23.0 MB
EGAF00005002440 idx 2.8 MB
EGAF00005002441 vcf 20.9 MB
EGAF00005002442 idx 2.6 MB
EGAF00005002443 vcf 22.4 MB
EGAF00005002444 idx 3.2 MB
EGAF00005002445 vcf 22.5 MB
EGAF00005002446 idx 3.0 MB
EGAF00005002447 vcf 22.7 MB
EGAF00005002448 idx 2.7 MB
EGAF00005002449 vcf 20.7 MB
EGAF00005002450 idx 2.8 MB
204 Files (509.1 GB)