Genoox

* Using fewer than the recommended samples may reduce model quality and increase calling artifacts ​

** Small gene panels require the sample list file to include each reference sample's sex, particularly when the panel omits sex chromosome genes. 

Standardize sample preparation - all reference samples must use the same capture kit (for WES and panels), library preparation protocol, and sequencing platform. All future samples run against this model must follow the same protocol.

1. Samples should come from individuals free of known large chromosomal abnormalities
2. Avoid enrichment for specific diseases or genetic syndromes
3. Ideally, samples must be unrelated
4. Balanced distribution of sample sex (unless the sequencing panel does not include sex chromosomes)

High-quality samples - exclude low- or uneven-coverage samples.

Multiple sample batch - Use samples from multiple preparation batches and sequencing runs to minimize batch bias.

1. Standardize sample preparation - all reference samples must use the same capture kit (for WES and panels), library preparation protocol, and sequencing platform. All future samples run against this model must follow the same protocol. 
2. Biological Diversity: 
 1. Samples should come from individuals free of known large chromosomal abnormalities
 2. Avoid enrichment for specific diseases or genetic syndromes
 3. Ideally, samples must be unrelated
 4. Balanced distribution of sample sex (unless the sequencing panel does not include sex chromosomes) 
3. High-quality samples - exclude low- or uneven-coverage samples. 
4. Multiple sample batch - Use samples from multiple preparation batches and sequencing runs to minimize batch bias.

Rainbow CNV model requirements

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Assay Type	Recommended Number of Samples	Minimal Number of Samples*
WES / Large gene panel	30-60	20
Small gene panel (<1 mb)**	50-100	30
Somatic gene panel	50-100	30
Somatic gene panel + backbone	50-100	30
WGS	30-60	15
WGS + Homology genes haplotyping	30-60	20
WGS - Lowpass	30-60	20

Parameter	Assay Type	Options	Default	Description
Gene Scope	Somatic	True/False	False	When True, caps the size of called CNVs to a single gene. Use for panels with widely spaced covered regions (non-backbone kits)
Max Deletion CN	Somatic	0.1-1.9	≤ 1.0	Maximum copy-number threshold for a valid somatic deletion
Min Duplication CN	Somatic	2.1-10	≥ 2.8	Minimum copy-number threshold for a valid somatic duplication
WGS Homology Haplotyping	WGS	True/False	False	Homology haplotype calling for SMN and HBA
Mosaic Calling	WGS	True/False	True	Enable mosaic variant calling
Mosaic Level	WGS	0.2-0.8	0.4	Mosaic detection sensitivity threshold. At 0.4, only variants with CN ≥ 2.4 or CN ≤ 1.6 are called.

Rainbow CNV model requirements

Reference cohort selection

Cohort size requirements

Reference samples selection criteria

Model configurations