Table A3.

Study Design parameters influencing the construction of a research study and associated genetic toolbox are written and described in the table above.

Parameter	Symbol	Data Type	Description
Number of Samples	$s$	Samples	Number of distinct tissue biopsies to be drawn from each “tumor” site
Type of Sample	sample	None	Defines how a sample is taken from the cell population (generally solid or liquid biopsy, though other methods like liquid capture microdissection are less commonly used)
Number of sequencing protocols taken on the $i^{th}$ sample	$l_i$	Integer	Number of individual sequencing protocols taken on the sample $i$
Number of single cells used in a sequencing protocol	$n$	Integer	Number of single cells operated upon under a singular sequencing protocol. If zero, no single cells are generated and only bulk sequencing is performed.
Read Length	$rl$	Integer –number of Bases	Size of reads to be generated from sequencer
Fragment Length	$fl$	Integer –number of bases	Defines a superstring from which reads are derived during the sequencing process
Depth/Coverage	$c$	Integer – reads per Base	Average number of times each nucleotide of the genome is sequenced
Error Rate	$e$	Float – Fraction of Incorrectly Sequenced Bases	Rate of Incorrectly sequenced nucleotides
Paired-End/Single-end	Paired	Boolean	Binary parameter describing whether the reads are paired end or single end. Paired-end reads have two related reads derived from the same fragment.
Whole Genome/Whole Exome/Targeted Sequencing	Genome	Boolean	Binary parameter describing whether the sequencer extracts genes from the entire genome or only a subset of the genome
Informatics Tools	Informatics	Categorical/numerical	A parameter describing the type of informatics software used to analyze a sequencing protocol for information. Notably the encoding is flexible, and could be represented many different ways.