Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

This study compared different assays for the detection of circulating tumour DNA (ctDNA) in serial plasma from stage IA-IV breast cancer patients, targeting structural variants (SVs), single nucleotide variants (SNVs) and/or somatic copy-number aberrations (SCNAs). SV-multiplex PCR, SNV-/SV-hybrid capture, and different depths of whole-genome sequencing (WGS) were used to evaluate ctDNA levels, demonstrating concordant results. SNV-hybrid capture targeting 1,347-7,491 mutations was the most sensitive assay, detecting 67% (36/54) of samples down to an allele fraction (AF) of 0.00024%. SV-multiplex PCR, targeting 21-47 mutations, detected 63% (34/54) of samples down to 0.00047% AF and has potential as a clinical assay.

1284 samples
DAC: EGAC00001002549
Technologies: HiSeq X Ten, Illumina HiSeq 4000, Illumina MiSeq, Illumina NovaSeq 6000

Access Policy1 Study Files

Metadata

Request Access

Policy for access to data included in the following publication; Comparison of multiplex PCR, hybrid capture and whole-genome sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

~~~ Definitions: Confidential Information: means any information provided by the Data Provider relating to the Data Data: The managed access dataset(s) to which the User Institution has requested access, as detailed in Schedule B. Data Provider: THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE of The Old Schools, Trinity Lane, Cambridge CB2 1TN, United Kingdom and the Cambridge University Hospitals NHS Foundation Trust of Addenbrooke’s Hospital, Cambridge, CB2 0QQ; represented by staff of the Rosenfeld Group at the Cancer Research UK Cambridge Institute, and contactable by email at Rosenfeld.LabAdmin@cruk.cam.ac.uk or future email as updated; or future representatives as indicated in Data Access Committee(s) for the dataset(s) defined in Schedule B. Data Subject: means an individual who participated in research studies from whom the Data was derived. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. 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Data Provider will provide access to Data to the User Institution under the following Terms and Conditions: 1. You agree to preserve, at all times, the confidentiality and privacy of information and Data pertaining to Data Subjects. In particular, you undertake not to use, or attempt to use the Data to compromise or otherwise breach or infringe the confidentiality and privacy of information on Data Subjects. You agree to protect the confidentiality of Data Subjects in any Publications that you prepare by taking all reasonable care to limit the possibility of identification. You agree not to attempt to link Data to any other data source on the same samples, link the Data to any person or otherwise identify any Data Subject from the Data. 2. You agree not to transfer or disclose the Data, in whole or part, to others, except to persons within the User Institution for carrying out the Project or as reasonably necessary for Data/safety monitoring or programme management. 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(d) For the avoidance of doubt, You undertake not to disclose to a third party, whether in connection with the Project or otherwise, any data and/or information contained in or derived from the Data which constitutes Personal Data. 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Schedule B Name of the applicant and co-applicant(s), including affiliations, titles and contact details. For dataset deposited at EGA, applicants must have registered accounts at EGA. Student applicants must include their supervisors as a co-applicant. Name of registered user; Email; Job title; Supervisor*; Title of Project (in less than 30 words) Data Requested (please indicate relevant publication(s) describing the data, accession number(s) and/or relevant links to data, and [where relevant] details of and links to the respective Data Access Committee(s) (DAC)) Research Project: Please provide a clear description of the project and its specific aims in no more than 750 words. This should include specific details of what you plan to do with the data and include key references. Brief description of the infrastructure and experience for handling the requested data securely Signature of authorized signatory of User Institution Signature; Name; Title; Date; Signature of Principal Investigator I confirm that I have read and understood the TERMS AND CONDITIONS as set forth in this DATA ACCESS REQUEST FORM. Signature; Name; Title; Date; ~~~~~~~ Data Access Request Form, V1 CRUK-CI, Rosenfeld Lab, July 2019

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
EGAS00001006040	Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer	Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID	File Type	Size
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EGAF00005806437	fq.gz	1.7 GB
EGAF00005806438	fq.gz	1.9 GB
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EGAF00005806442	fq.gz	4.5 MB
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EGAF00005806444	fq.gz	9.7 MB
EGAF00005806445	fq.gz	10.7 MB
EGAF00005806446	fq.gz	12.0 MB
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EGAF00005806448	fq.gz	7.8 MB
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EGAF00005806450	fq.gz	9.3 MB
EGAF00005806451	fq.gz	3.1 MB
EGAF00005806452	fq.gz	3.3 MB
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EGAF00005806454	fq.gz	11.2 MB
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EGAF00005806456	fq.gz	8.3 MB
EGAF00005806457	fq.gz	1.7 GB
EGAF00005806458	fq.gz	1.9 GB
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EGAF00005806461	fq.gz	9.9 MB
EGAF00005806462	fq.gz	10.8 MB
EGAF00005806463	fq.gz	125.2 MB
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EGAF00005806474	fq.gz	13.2 MB
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EGAF00005806476	fq.gz	3.9 MB
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EGAF00005806482	fq.gz	16.2 MB
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EGAF00005806484	fq.gz	5.9 MB
EGAF00005806485	fq.gz	6.1 MB
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EGAF00005806488	fq.gz	9.2 MB
EGAF00005806489	fq.gz	8.9 MB
EGAF00005806490	fq.gz	9.5 MB
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EGAF00005806492	fq.gz	2.9 MB
EGAF00005806493	fq.gz	1.2 GB
EGAF00005806494	fq.gz	1.4 GB
EGAF00005806495	fq.gz	13.8 MB
EGAF00005806496	fq.gz	14.8 MB
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EGAF00005806498	fq.gz	7.5 MB
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EGAF00005806517	fq.gz	13.8 MB
EGAF00005806518	fq.gz	14.4 MB
EGAF00005806519	fq.gz	1.7 GB
EGAF00005806520	fq.gz	2.0 GB
EGAF00005806521	fq.gz	1.3 GB
EGAF00005806522	fq.gz	1.4 GB
EGAF00005806523	fq.gz	3.7 MB
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EGAF00005806525	fq.gz	9.4 MB
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EGAF00005806545	fq.gz	2.3 MB
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EGAF00005806550	fq.gz	11.6 MB
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EGAF00005806552	fq.gz	11.7 MB
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EGAF00005806583	fq.gz	136.1 MB
EGAF00005806584	fq.gz	274.5 MB
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EGAF00005806587	fq.gz	9.2 MB
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EGAF00005806590	fq.gz	10.7 MB
EGAF00005806591	fq.gz	1.4 GB
EGAF00005806592	fq.gz	1.7 GB
EGAF00005806593	fq.gz	4.3 MB
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EGAF00005806597	fq.gz	942.4 kB
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EGAF00005806803	fq.gz	476.4 kB
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EGAF00005806839	fq.gz	1.7 GB
EGAF00005806840	fq.gz	1.9 GB
EGAF00005806841	fq.gz	14.2 MB
EGAF00005806842	fq.gz	15.0 MB
EGAF00005806843	fq.gz	266.1 kB
EGAF00005806844	fq.gz	283.5 kB
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EGAF00005806898	fq.gz	2.2 GB
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EGAF00005806939	fq.gz	10.1 GB
EGAF00005806940	fq.gz	10.5 GB
EGAF00005806941	fq.gz	250.7 MB
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EGAF00005806952	fq.gz	19.0 MB
EGAF00005806953	fq.gz	3.5 GB
EGAF00005806954	fq.gz	3.6 GB
EGAF00005806955	fq.gz	377.8 kB
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EGAF00005806973	fq.gz	1.3 GB
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EGAF00005806983	fq.gz	714.8 kB
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EGAF00005806987	fq.gz	1.7 GB
EGAF00005806988	fq.gz	1.9 GB
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EGAF00005807011	fq.gz	7.8 MB
EGAF00005807012	fq.gz	8.8 MB
EGAF00005807013	fq.gz	28.2 MB
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EGAF00005807269	fq.gz	826.4 MB
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EGAF00005807282	fq.gz	211.5 MB
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EGAF00005807369	fq.gz	785.6 kB
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EGAF00005807437	fq.gz	1.3 GB
EGAF00005807438	fq.gz	1.5 GB
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EGAF00005807471	fq.gz	974.9 kB
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EGAF00005807493	fq.gz	8.1 MB
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EGAF00005807690	fq.gz	985.1 kB
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EGAF00005807745	fq.gz	6.1 MB
EGAF00005807746	fq.gz	129.3 MB
EGAF00005807747	fq.gz	259.6 MB
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EGAF00005807749	fq.gz	11.4 MB
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EGAF00005807768	fq.gz	134.4 MB
EGAF00005807769	fq.gz	272.0 MB
EGAF00005807770	fq.gz	1.5 GB
EGAF00005807771	fq.gz	1.9 GB
EGAF00005807772	fq.gz	2.2 MB
EGAF00005807773	fq.gz	2.4 MB
EGAF00005807774	fq.gz	10.0 MB
EGAF00005807775	fq.gz	10.6 MB
EGAF00005807776	fq.gz	1.5 GB
EGAF00005807777	fq.gz	1.7 GB
EGAF00005807778	fq.gz	1.9 MB
EGAF00005807779	fq.gz	2.0 MB
EGAF00005807780	fq.gz	2.7 MB
EGAF00005807781	fq.gz	2.9 MB
EGAF00005807782	fq.gz	9.6 MB
EGAF00005807783	fq.gz	10.7 MB
EGAF00005807784	fq.gz	11.6 MB
EGAF00005807785	fq.gz	12.7 MB
EGAF00005807786	fq.gz	9.2 MB
EGAF00005807787	fq.gz	9.8 MB
EGAF00005807788	fq.gz	13.6 MB
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EGAF00005807790	fq.gz	10.9 MB
EGAF00005807791	fq.gz	11.5 MB
EGAF00005807792	fq.gz	8.6 MB
EGAF00005807793	fq.gz	9.3 MB
EGAF00005807794	fq.gz	8.5 MB
EGAF00005807795	fq.gz	9.3 MB
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EGAF00005807797	fq.gz	6.8 MB
EGAF00005807798	fq.gz	13.2 MB
EGAF00005807799	fq.gz	14.0 MB
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EGAF00005807801	fq.gz	6.8 MB
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EGAF00005807812	fq.gz	12.4 MB
EGAF00005807813	fq.gz	13.1 MB
EGAF00005807814	fq.gz	10.3 GB
EGAF00005807815	fq.gz	10.6 GB
EGAF00005807816	fq.gz	293.9 MB
EGAF00005807817	fq.gz	637.4 MB
EGAF00005807818	fq.gz	1.5 GB
EGAF00005807819	fq.gz	1.7 GB
EGAF00005807820	fq.gz	7.0 MB
EGAF00005807821	fq.gz	7.3 MB
EGAF00005807822	fq.gz	5.0 MB
EGAF00005807823	fq.gz	5.3 MB
EGAF00005807824	fq.gz	5.3 MB
EGAF00005807825	fq.gz	5.7 MB
EGAF00005807826	fq.gz	22.4 MB
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EGAF00005807829	fq.gz	11.8 MB
EGAF00005807830	fq.gz	14.3 MB
EGAF00005807831	fq.gz	15.3 MB
EGAF00005807832	fq.gz	10.3 MB
EGAF00005807833	fq.gz	11.3 MB
EGAF00005807834	fq.gz	1.4 GB
EGAF00005807835	fq.gz	1.7 GB
EGAF00005807836	fq.gz	1.0 MB
EGAF00005807837	fq.gz	1.1 MB
EGAF00005807840	fq.gz	11.4 MB
EGAF00005807841	fq.gz	12.8 MB
EGAF00005807842	fq.gz	10.5 MB
EGAF00005807843	fq.gz	11.2 MB
EGAF00005807844	fq.gz	11.4 MB
EGAF00005807845	fq.gz	12.1 MB
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EGAF00005807848	fq.gz	1.4 MB
EGAF00005807849	fq.gz	1.4 MB
EGAF00005807850	fq.gz	2.6 MB
EGAF00005807851	fq.gz	2.7 MB
EGAF00005807852	fq.gz	19.1 MB
EGAF00005807853	fq.gz	20.5 MB
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EGAF00005807855	fq.gz	8.5 MB
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EGAF00005807866	fq.gz	8.4 MB
EGAF00005807867	fq.gz	9.3 MB
EGAF00005807868	fq.gz	6.2 MB
EGAF00005807869	fq.gz	6.6 MB
EGAF00005807870	fq.gz	1.5 GB
EGAF00005807871	fq.gz	1.8 GB
EGAF00005807872	fq.gz	7.6 MB
EGAF00005807873	fq.gz	8.2 MB
EGAF00005807874	fq.gz	10.2 MB
EGAF00005807875	fq.gz	11.5 MB
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EGAF00005807879	fq.gz	8.8 MB
EGAF00005807880	fq.gz	121.2 MB
EGAF00005807881	fq.gz	244.2 MB
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EGAF00005807897	fq.gz	17.2 MB
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EGAF00005807902	fq.gz	87.4 MB
EGAF00005807903	fq.gz	181.8 MB
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EGAF00005807907	fq.gz	13.3 MB
EGAF00005807908	fq.gz	1.9 GB
EGAF00005807909	fq.gz	2.2 GB
EGAF00005807910	fq.gz	6.4 MB
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EGAF00005807912	fq.gz	12.4 MB
EGAF00005807913	fq.gz	13.8 MB
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EGAF00005807919	fq.gz	3.5 MB
EGAF00005807920	fq.gz	1.1 GB
EGAF00005807921	fq.gz	1.2 GB
EGAF00005807924	fq.gz	120.3 MB
EGAF00005807925	fq.gz	262.3 MB
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EGAF00005807929	fq.gz	588.9 MB
EGAF00005807930	fq.gz	3.7 GB
EGAF00005807931	fq.gz	3.9 GB
EGAF00005807932	fq.gz	17.0 MB
EGAF00005807933	fq.gz	18.0 MB
EGAF00005807934	fq.gz	13.1 MB
EGAF00005807935	fq.gz	14.0 MB
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EGAF00005807938	fq.gz	23.1 MB
EGAF00005807939	fq.gz	24.9 MB
EGAF00005807940	fq.gz	12.8 GB
EGAF00005807941	fq.gz	13.2 GB
EGAF00005807942	fq.gz	106.4 MB
EGAF00005807943	fq.gz	206.7 MB
EGAF00005807944	fq.gz	9.7 MB
EGAF00005807945	fq.gz	10.5 MB
EGAF00005807946	fq.gz	7.8 MB
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EGAF00005807983	fq.gz	2.4 MB
EGAF00005807984	fq.gz	1.7 GB
EGAF00005807985	fq.gz	2.1 GB
EGAF00005807986	fq.gz	1.1 GB
EGAF00005807987	fq.gz	1.2 GB
EGAF00005807988	fq.gz	1.4 MB
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EGAF00005807994	fq.gz	975.3 kB
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EGAF00005808155	fq.gz	19.8 MB
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EGAF00005808157	fq.gz	11.2 MB
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EGAF00005808165	fq.gz	5.5 MB
EGAF00005808166	fq.gz	807.1 MB
EGAF00005808167	fq.gz	1.9 GB
EGAF00005808168	fq.gz	1.1 MB
EGAF00005808169	fq.gz	1.2 MB
EGAF00005808170	fq.gz	2.3 MB
EGAF00005808171	fq.gz	2.5 MB
EGAF00005808172	fq.gz	91.1 MB
EGAF00005808173	fq.gz	175.9 MB
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EGAF00005808177	fq.gz	8.2 MB
EGAF00005808178	fq.gz	5.2 MB
EGAF00005808179	fq.gz	5.7 MB
EGAF00005808180	fq.gz	1.2 GB
EGAF00005808181	fq.gz	1.5 GB
EGAF00005808182	fq.gz	7.3 MB
EGAF00005808183	fq.gz	7.7 MB
EGAF00005808184	fq.gz	11.5 MB
EGAF00005808185	fq.gz	12.3 MB
EGAF00005808186	fq.gz	9.1 MB
EGAF00005808187	fq.gz	9.7 MB
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EGAF00005808192	fq.gz	1.5 GB
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EGAF00005808206	fq.gz	896.4 kB
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EGAF00005808220	fq.gz	100.2 MB
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EGAF00005808473	fq.gz	3.8 GB
EGAF00005808474	fq.gz	8.7 MB
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EGAF00005808476	fq.gz	70.2 MB
EGAF00005808477	fq.gz	146.2 MB
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EGAF00005808483	fq.gz	2.0 GB
EGAF00005808484	fq.gz	13.1 MB
EGAF00005808485	fq.gz	14.0 MB
EGAF00005808486	fq.gz	949.1 MB
EGAF00005808487	fq.gz	2.2 GB
EGAF00005808488	fq.gz	9.2 MB
EGAF00005808489	fq.gz	9.7 MB
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EGAF00005808491	fq.gz	9.1 MB
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EGAF00005808501	fq.gz	149.0 MB
EGAF00005808502	fq.gz	11.8 MB
EGAF00005808503	fq.gz	12.3 MB
EGAF00005808504	fq.gz	1.8 GB
EGAF00005808505	fq.gz	2.0 GB
EGAF00005808506	fq.gz	107.3 MB
EGAF00005808507	fq.gz	210.0 MB
EGAF00005808508	fq.gz	2.7 MB
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EGAF00005808510	fq.gz	3.7 GB
EGAF00005808511	fq.gz	3.8 GB
EGAF00005808514	fq.gz	7.8 MB
EGAF00005808515	fq.gz	8.2 MB
2760 Files (663.3 GB)