Table Info

Table 1.

TRG gene segment usage as indicated by the recovery of TRG recombination reads from exome or RNAseq files

Source of recombination reads	Disease	Blood or other tissue processed	*Fraction V9 of all TRG* recombination reads**	*Fraction JP of all TRG* recombination reads**	*Fraction V9-JP recombination of all TRG* recombination reads**	Two-proportion test comparing V9-JP percentages, for ALS/PD	Fraction retention of JP KKIK motif	SOM file	Project
TRG recombination reads mined from exome files	ALS, familial	Blood	15/16	16/16	15/16	The data in preceding column of this row is used for below 2-proportion tests, left-side value in succeeding rows	16/16	Table S1	phs000101
	PD	Blood	33/37	37/37	33/37	The data of the preceding column of this row is used for below 2-proportion tests, right-side value in succeeding rows	35/37	Table S2	phs001172
	ESCA	Blood	23/136	5/136	5/136	< 0.0001/< 0.0001	5/5	Table S3	TCGA-ESCA
	LUSC	Blood	74/493	23/493	20/493	< 0.0001/< 0.0001	22/23	Table S4	TCGA-LUSC
	COAD	Blood	55/239	23/239	21/239	< 0.0001/< 0.0001	20/23	Table S5	TCGA-COAD
	STAD	Blood	102/449	41/449	30/449	< 0.0001/< 0.0001	40/41	Table S6	TCGA-STAD
	Melanoma	Blood	223/953	81/953	72/953	< 0.0001/< 0.0001	81/81	Table S7	TCGA-SKCM
	Multiple myeloma	Blood	1,007/9,081	223/9,081	134/9,081	< 0.0001/< 0.0001	207/223	Table S8	COMPASS-MMRF
	WT	Blood	113/620	19/620	11/620	< 0.0001/< 0.0001	17/19	Table S9	TARGET-WT
	NBL	Blood	283/725	138/725	129/725	< 0.0001/< 0.0001	135/138	Table S10	TARGET-NBL
TRG recombination reads mined from RNAseq files	ALS	Blood	11,381/29,170	6,189/29,170	6,078/29,170	The data of the preceding column in this row is used for the 2-proportion tests in succeeding rows	6,014/6,189	Table S11	phs002055
	WT	Tumor	28/65	11/65	11/65	NS/NA	11/11	Table S12	TARGET-WT
	DLBCL	Lymph node	2,169/9,911	253/9,911	211/9,911	< 0.0001/NA	233/253	Table S13	NCICCR-DLBCL
	NBL	Tumor	456/1,799	99/1,799	98/1,799	< 0.0001/NA	98/99	Table S14	TARGET-NBL

All 2-proportion test comparisons of ALS and PD are with non-neurological diseases, and the recovery of all TRG recombination reads are in the SOM Tables. Note, WXS results were compared to WXS results; RNAseq results were compared to RNAseq results (Table S15). Phs numbers can be accessed at dbGaP. The acronyms in the last column are defined here and at the genomic data commons. NS: not significant; NA: not applicable; TCGA: The Cancer Genome Atlas; ESCA: esophageal cancer; LUSC: lung squamous cell carcinoma; COAD: colon adenocarcinoma; STAD: stomach adenocarcinoma; SKCM: skin cutaneous melanoma; MMRF: Multiple Myeloma Research Foundation; TARGET: Therapeutically Applicable Research to Generate Effective Treatment; WT: Wilms tumor; NCICCR: National Cancer Institute Center for Cancer Research; DLBCL: diffuse large B-cell lymphoma; NBL: neuroblastoma

Supplementary materials

The supplementary Tables for this article are available at: https://www.explorationpub.com/uploads/Article/file/1003124_sup_1.xlsx and https://www.explorationpub.com/uploads/Article/file/1003124_sup_2.pdf.

Declarations

Acknowledgments

Authors thank Ms. Corinne Walters for administrative support for database access, USF research computing, and the taxpayers of the State of Florida. Bryan J. Traynor was the principal investigator for the ALS study, phs000101. Matthew Harms was the principal investigator for the ALS study, phs002055. The principal investigators of the other studies of Table 1 can be identified via the study information in Table 1 and the use of the https://www.ncbi.nlm.nih.gov/gap/ search page.

Author contributions

GB: Conceptualization, Supervision, Formal analysis, Methodology, Visualization, Writing—review & editing. TIH: Conceptualization, Formal analysis, Methodology, Software. KJC: Formal analysis, Methodology. GA: Formal analysis, Methodology, Writing—review & editing. JJS: Formal analysis, Methodology, Software.

Conflicts of interest

The authors declare that there are no conflicts of interest.

Ethical approval

Not applicable.

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

The dataset genomics files were accessed according dbGaP approvals listed for George Blanck (according to the dataset identifying information in Table 1) at https://www.ncbi.nlm.nih.gov/gap/. Other data are included in the manuscript and the supplementary files.

Funding

Not applicable.

Copyright

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