Table 1 Classification of B-other-ALL by standard and NGS techniques.

From: Integrative genomic analysis of childhood acute lymphoblastic leukaemia lacking a genetic biomarker in the UKALL2003 clinical trial

Genomic Subtype	Abnormality	Standard techniques	NGS
ABL-class	*ABL1* fusion	ABL1, ABL2, PDGFRB or CSF1R rearrangement by FISH	ABL1, ABL2, PDGFRB or CSF1R fusion
	*ABL2* fusion
	*CSF1R* fusion
	*PDGFRB* fusion
**ETV6::RUNX1-like**	*ETV6* rearrangement	ETV6 rearrangement by FISH	ETV6 fusion
	*IKZF1* rearrangement	IKZF1 rearrangement by FISH	IKZF1 fusion and/or deletion
	Other **ETV6::RUNX1-like**	Not applicable	ETV6 biallelic inactivation in patients that lack other defining features
*IGH::ID4*		t(6;14)(p22;q32) by karyotype and/or IGH::ID4 positive by FISH	IGH::ID4
*CRLF2*-r	*IGH::CRLF2*	IGH::CRLF2 positive by FISH	IGH::CRLF2
*CRLF2*-r	*P2RY8::CRLF2*	P2RY8::CRLF2 by FISH and/or PAR1 deletion by MLPA or SNP array	P2RY8::CRLF2
*JAK2*-r		JAK2 rearrangement by FISH	JAK2 fusion
*ZNF384-r*		ZNF384 rearrangement by FISH	ZNF384 fusion
*MEF2D*-r		MEF2D rearrangement by FISH	MEF2D fusion by WGS*
*NUTM1*-r		NUTM1 rearrangement by FISH	NUTM1 fusion
**PAX5alt**	*PAX5* rearrangement	PAX5 rearrangement by FISH	PAX5 fusion
	**PAX5-ITD**	Internal Tandem Duplication (Amplification) of PAX5 exons 2–5 by MLPA or SNP array	PAX5-ITD by NGS
	*PAX5* mutation	Not applicable	Clonal PAX5 mutation (VAF = > 35%) not P80R that lack other defining features
	dic(9;20)	dic(9;20) by karyotype or loss of 9p and 20p by SNP array	dic(9;20) i.e. loss of 9p and 20p and/or PAX5::NOL4L
	dic(9;12)	dic(9;12) by karyotype or loss of 9p and 12p with retention of 5’PAX5 and 3’ETV6 by SNP array	dic(9;12) i.e. loss of 9p and 12p and PAX5::ETV6
	Other **PAX5alt**	Not applicable	Biallelic inactivation of PAX5 or PAX5 loss [CN = 1] in cases with biallelic CDKN2A/B loss [CN = 0], and MTAP CNV/SV [CN = 0/1] that lack other defining features
*IKZF1* N159Y		Not applicable	IKZF1 N159Y mutation and/or IKZF-ITD (Internal Tandem Duplication)
*PAX5* P80R		Not applicable	PAX5 P80R mutation
*BCL2/MYC*		IGH::BCL2 and/or IGH::MYC positive by FISH	Gene rearrangement involving BCL2, BCL6 or MYC
*DUX4*-r	*DUX4*-r	Not applicable	DUX4 rearrangement by WGS*
*DUX4*-r	*ERG-*d	Intragenic ERG deletion by MLPA or SNP array	Intragenic deletion, mutation or other rearrangement of ERG
*ZEB2/CEBP*		IGH::CEBP family gene positive by FISH	CEBP family gene rearrangement and/or ZEB2 H1038R mutation
*IGH::IL3*		t(5;14)(q31;q32) by karyotype and/or IGH::IL3 positive by FISH	IGH::IL3

Standard-of-care techniques include cytogenetics, FISH, MLPA and SNP array. NGS includes WGS and t-NGS. Abnormal FISH signal patterns classed as balanced rearrangements: 1R1G1F, or unbalanced: 1R0G1F or 0R1G1F, with evidence of fusion from karyotype, partner gene FISH, SNP array or RT-PCR, as previously published [12]. MEF2D::CSF1R and ETV6::ABL1 are classified as ABL-class fusions, PAX5::JAK2 and ETV6::JAK2 are classified as JAK2-r, PAX5::ETV6 are classified as PAX5alt according to previously published data [2]. All other rearrangements of ETV6 are assigned to the ETV6::RUNX1-like subtype. PAX5 mutations and CN abnormalities of PAX5, CDKN2A/B and MTAP are classified as PAX5alt, only in the absence of other subtype defining abnormalities. *DUX4 and MEF2D were not included in the t-NGS kit. CN copy number, SV structural variant, CNV copy number variant.

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Table 1 Classification of B-other-ALL by standard and NGS techniques.

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