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Number of participants Number of participations
EXTERNAL QUALITY ASSESSMENT
Fig 1. Number of participants and participations on GENie since 2023.
newly introduced 2024 ISCN guidelines. To support individuals analysing the vast amount of genomic data generated by sequencing, a GENie module assessing Whole Genome Sequencing and Whole Exome Sequencing proportionate variant analysis was launched in April 2025. Later in 2025, two more modules were introduced to further support the role of a geneticist which will cover risk calculations for autosomal recessive and X-linked recessive conditions and somatic variant classification covering solid tumours and haemato-oncology.
HGVS nomenclature modules A total of 1,383 participants have completed the HGVS nomenclature modules between June 2023 and April 2025. GENie began with two HGVS nomenclature trials that were conducted for the first 18 months, during which 822 participants completed both trials. Overall, adherence to HGVS nomenclature1
was high, with eight
variants being accurately described by over than 150 participants each, except for variant 1 and variant 5 from the first trial (Fig 2). Figure 2 also summarises the most common types of errors observed. Variant 8 had the highest error rate, mainly due to participants listing the reference sequences in the incorrect order, listing the NM record before the NC record. A similar error pattern was observed with variant 5. Other frequent
errors included omission of the reference sequence version number or inclusion of the deleted bases. In order to deliver competency assessment to the full workforce, as of November 2024, a new series of nomenclature modules was released that targets all levels of knowledge (basic, intermediate and advanced). Overall, 561 participants have completed the HGVS basic module. Each module contains five cases; therefore 822 submissions have been reported. Of these, 676 (82%) participants provided the correct nomenclature, and 146 (18%) participants provided the incorrect answers. The highest error rate (20%)
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0 1 2 3 4 Fig 2. Results of the HGVS Nomenclature trials.
WWW.PATHOLOGYINPRACTICE.COM DECEMBER 2025 45 5 6 Variants 7 8 9 10
Correct answer(s) Most frequent error
occurred when participants didn’t use the correct format for alleles. Interestingly, another common error (seen in 10% of participations) was the omission of the predicted protein change in parentheses, an error that did not occur during the first two trials.
ISCN modules
A total of 1,750 participants completed the ISCN modules between June 2023 and April 2025. The ISCN modules were initially offered as trials and participants generally demonstrated consistency with the application of ISCN 2020 for reporting microarray results and Neoplasia karyotyping results.
BRCA1, BRCA2 and HRR gene variant classification (Run11)
BRCA1, BRCA2 and HRR gene variant classification (Run12)
BRCA1, BRCA2 and HRR gene variant classification (Run13)
BRCA1, BRCA2 and HRR gene variant classification (Run14)
GENie assessment for WGS/WES proportionate variant analysis
GENie Germline CNV classification
GENie Germline SNV classification
GENie Trial: Germline CNV classification
Number of participants
GENie Trial: Germline SNV classification
GENie Trial 2: Germline CNV classification
GENie Trial 2: Germline SNV classification
GENie Trial: HGVS nomenclature
GENie Trial 2: HGVS nomenclature
GENie HGVS nomenclature basic
GENie Trial: ISCN nomenclature
GENie Trial 2: ISCN nomenclature
GENie ISCN constitutional FISH basic
GENie ISCN constitutional karyotyping basic
GENie ISCN neoplasia karyotyping basic
GLH CVS and amniocentesis sample processing
DNA extraction GLH
laboratory tour RNA extraction
GLH SNP and CGH array
GLH whole genome sequencing
GLH NIPT GLH
GLH
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