Dataset Information

Phase One Resequencing for 10,000 Dog Genome Consortium

ABSTRACT: The international Dog10K consortium (Dog10K) was established to capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. The VCF was produced using a BWA-GATK best practices pipeline and input sequences of greater than 10x coverage.

INSTRUMENT(S): Illumina HiSeq X Ten

ORGANISM(S): Canis Lupus Familiaris

SUBMITTER: Uppsala University

PROVIDER: PRJEB62420 | EVA | 2023-05-21

REPOSITORIES: EVA

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Dataset's files

Source:

			Action	DRS
	Dog10K_phase1_merged.accessioned.vcf.gz	Vcf
	Dog10K_phase1_merged.accessioned.vcf.gz.csi	Vcf
	Dog10K_phase1_merged.vcf.csi	Other
	Dog10K_phase1_merged.vcf.gz	Vcf

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Project description:The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is to develop standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight common ground in a diverse landscape of different sample preparation techniques and LC-MS setups with the aim to explore differences and potential confounding factors as well as to identify areas for improvement with a direct practical benefit. With the aim to benchmark and improve current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium we performed two consecutive round robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six participating study partners were provided with two clinically relevant sample matrices: plasma, and cerebrospinal fluid (CSF). In the first round each laboratory applied their current best practice protocol for the respective matrix, covering laboratory-specific sample proteolysis, liquid chromatography, and MS measurement procedure. All resulting MS files were analyzed centrally by a standardized pipeline. Based on the achieved results and following a fully transparent exchange of all lab-specific protocols within the consortium, each laboratory could improve their methods before measuring the same samples in a second acquisition round. The results of both measurement time points are compared with respect to identifications (IDs), data completeness, retention time and quantitative precision as well as inter-laboratory reproducibility. For instance, the number of identified protein groups was increased on average by 14% for CSF and 5% for plasma from first to second measurement round across participants resulting in a median overlap number of 579 protein groups for CSF and 246 IDs for plasma across setups. The individual performances of participating study centers and the inter-laboratory reproducibility were improved in the second measurement, emphasizing the effect and importance of expert-driven exchange of best practices. In total, the study not only clearly demonstrates the beneficial effect of sharing knowledge and expertise for direct practical improvements but also highlights tendencies such as common limits of detection or preferable preparation strategies.

Dataset Information

Phase One Resequencing for 10,000 Dog Genome Consortium

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