Create table 2

[jharenza]

Per this comment and PR, we are adding a main table 2 to the manuscript and it has not been entirely created yet. Below are some of the details.

Looks good! We may need to create Table 2 though, unless I am not seeing it somewhere?

Not entirely created - you created a portion here, but I realized there was a cell line instead of tumor in that. Final table is the same samples from here, so we can definitely create in that notebook. The caveats are just renaming column names and that Therapy post-biopsy and the predispositions will have to be manually added and edited, respectively, because I had to look them up in another database and from path reports. I can create a ticket.

Just one suggestion to fix the spelling error!

Thanks!

Originally posted by @jharenza in https://github.com/AlexsLemonade/OpenPBTA-manuscript/issues/238#issuecomment-1099463922

Pasting the markdown version of this for the manual updates which will be required:

Kids First Participant ID	Kids First Biospecimen ID	CBTN ID	Phase of therapy	Therapy post-biopsy	Cancer predisposition(s)	TMB	OpenPBTA molecular subtype
PT_0SPKM4S8	BS_VW4XN9Y7	7316-2640	Initial CNS Tumor	Temozolomide, CCNU, Radiation	None documented	187.39	HGG, H3 wildtype, TP53 activated
PT_3CHB9PK5	BS_20TBZG09	7316-515	Initial CNS Tumor	Temozolomide, Irinotecan, Bevacizumab, Radiation	NF-1, Other inherited conditions NOS	307.05	HGG, H3 wildtype, TP53 loss
	BS_8AY2GM4G	7316-2085	Progressive	Unknown	NF-1, Lynch syndrome, pathogenic MSH6	321.61	HGG, H3 wildtype, TP53 loss
PT_JNEV57VK	BS_85Q5P8GF	7316-2594	Initial CNS Tumor	Temozolomide, Radiation	Lynch syndrome	4.73	DMG, H3 K28, TP53 loss
	BS_P0QJ1QAH	7316-3058	Progressive	Nivolumab	Lynch Syndrome, pathogenic MSH2	6.27	DMG, H3 K28, TP53 loss
PT_S0Q27J13	BS_P3PF53V8	7316-2307	Initial CNS Tumor	Temozolomide, Irinotecan, Radiation	None documented	15.48	HGG, H3 wildtype, TP53 activated
PT_VTM2STE3	BS_02YBZSBY	7316-2189	Progressive	Unknown	Lynch syndrome	274.49	HGG, H3 wildtype, TP53 activated

Table 2. Patients with hypermutant tumors. {#tbl:hypermutant}

Therapies are not currently in the histologies file, but were captured from the internal CBTN all database at https://d3b-rstudio-connect-public-prd.d3b.io/connect/#/apps/14d0e1b7-ab34-4dfc-bdbb-e1ee0f5325b7/access

The additional cancer predisposition of Lynch syndrome and pathogenic variants were manually curated via manual pathology report review by @jharenza

[jharenza]

I will work on this today

[sjspielman]

Closed with #1326