Biotinidase biochemical and molecular analyses: Experience at a large reference laboratory

BACKGROUND

Biotinidase deficiency is caused by absent activity of the biotinidase, encoded by the biotinidase gene (BTD). Affected individuals cannot recycle the biotin, leading to heterogeneous symptoms that are primarily neurological and cutaneous. Early treatment with biotin supplementation can prevent irreversible neurological damage and is recommended for patients with profound deficiency, defined as enzyme activity <10% mean normal (MN). Molecular testing has been utilized along with biochemical analysis for diagnosis and management. In this study, our objective was to correlate biochemical phenotype/enzyme activity to BTD genotype in patients for whom both enzyme and molecular testing were performed at our lab, and to review how the correlations inform on variant severity.

METHODS

We analyzed results of biotinidase enzyme analysis and BTD gene sequencing in 407 patients where samples were submitted to our laboratory from 2008 to 2020.

RESULTS

We identified 84 BTD variants; the most common was c.1330G>C, and 19/84 were novel BTD variants. A total of 36 patients had enzyme activity <10% of MN and the most common variant found in this group was c.528G>T. No variant was reported in one patient in the profound deficiency group. The most common variant found in patients with enzyme activity more than 10% MN was c.1330G>C.

CONCLUSIONS

Although enzyme activity alone may be adequate for diagnosing profound biotinidase deficiency, molecular testing is necessary for accurate carrier screening and in cases where the enzyme activity falls in the range where partial deficiency and carrier status cannot be discriminated.

Abstract PS16-02: Moving in the fast lane: Test design and validation to produce up-to-date hereditary breast and gynecologic cancer tests

Introduction

Germline genetic testing is increasingly relevant to breast and gynecologic (GYN) cancer clinicians for monitoring and managing high-risk patients. In particular, multi-gene panels (MGPs) can identify unsuspected cancer syndromes and variants that may become clinically significant. Effective MGPs must be comprehensive and up-to-date. For the current study, we used a probe panel designed for targeted enrichment of 4,500 genes associated with various inherited diseases to develop and validate a 66-gene comprehensive hereditary cancer panel, including subsets of genes associated with breast and GYN cancers.

Materials and Methods

Genomic DNA was extracted and taken through next generation sequencing (NGS) library preparation to be sequenced on an Illumina NovaSeq instrument. Targeted capture-based enrichment with a long-range PCR (LR-PCR) component was used to interrogate all protein-coding exons, intron-exon splice sites (+/-10bp), as well as clinically relevant deep intronic, 5’UTR, and 3’UTR regions for single nucleotide variants (SNVs) and insertions/deletions (indels) of all genes of interest. Copy number variations (CNVs) were also interrogated for all applicable regions. Data analysis was performed using a proprietary in-house bioinformatics variant analysis pipeline.

For validation, samples from the Coriell Repository and more than 100 unique de-identified genomic DNA specimens from whole blood and saliva were analyzed for 17,911 variants in 508 genes. Variants were previously identified by orthogonal methods (in-house Sanger sequencing, CLIA validated NGS assays, and microarray). The well-characterized Genome in a Bottle (GIAB) NA12878 and Ashkenazim Trio samples (NA24149, NA24385, and NA24143) were also included. The analytic sensitivity (Positive Percent Agreement, %PPA) and specificity (Technical Positive Predictive Value, %TPPV and Negative Percent Agreement, %NPA) were determined for each variant type (SNV, indel, and CNV).

The 66-gene hereditary cancer panel includes genes that confer ≥2-fold increased risk or 5% lifetime risk for developing cancer (APC, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDKN1B, CDKN2A (p16, p14), CHEK2, DICER1, EGFR, EPCAM, FANCA, FANCC, FANCM, FH, FLCN, GALNT12, GREM1, HOXB13, MAX, MEN1, MET, MITF, MLH1, MRE11 (MRE11A), MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NTHL1, PALB2, PMS2, POLD1, POLE, POT1, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RECQL, RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMARCA4, SMAD4, STK11, SUFU, TMEM127, TP53, TSC1, TSC2, VHL, and XRCC2). Of these, 30 genes increase the lifetime risk of breast and/or GYN cancers and are also distributed among smaller phenotype-specific panels.

Results

The analytical sensitivity (%PPA) for SNVs and indels was 100.0% and 97.8% for CNVs. The overall specificity for SNVs, indels, and CNVs was &gt;99.0%. The %TPPV for SNVs, Indels, and CNVs was 100.0%, 99.3%, and 100.0%, respectively. The %NPA for SNVs, Indels, and CNVs was 100.0%. The %PPA, %TPPV, and %NPA for LR-PCR was 100.0%.

Conclusion

Validation of the 66-gene hereditary cancer panel demonstrated high analytical sensitivity and specificity. As additional gene-cancer associations are established, using an already designed and developed comprehensive 4,500 gene panel will expedite the process of updating panel tests to include relevant candidate genes, allowing clinicians and patients to benefit from up-to-date and comprehensive testing.

Citation Format: Taraneh E Angeloni, Anindya Bhattacharya, Linda L Cheng, Hansook K Chong, Kelli M Conlan, Christopher D Elzinga, Anna Gerasimova, David Grover, Andrew Grupe, Michael Hua, Domagoj Hodko, Krista Kazmierkiewicz, Rebecca E Nakles, Camille R Nery, Renius Owen, Dana M Goos-Root, Charles M Rowland, Alla Smolgovsky, Elaine C Weltmer, Ke Zhang, Felicitas L Lacbawan. Moving in the fast lane: Test design and validation to produce up-to-date hereditary breast and gynecologic cancer tests [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS16-02.

Cryptic transcription mediates repression of subtelomeric metal homeostasis genes

Nonsense-mediated mRNA decay (NMD) prevents the accumulation of transcripts bearing premature termination codons. Here we show that Saccharomyces cerevisiae NMD mutants accumulate 5'-extended RNAs (CD-CUTs) of many subtelomeric genes. Using the subtelomeric ZRT1 and FIT3 genes activated in response to zinc and iron deficiency, respectively, we show that transcription of these CD-CUTs mediates repression at the bona fide promoters, by preventing premature binding of RNA polymerase II in conditions of metal repletion. Expression of the main ZRT1 CD-CUT is controlled by the histone deacetylase Rpd3p, showing that histone deacetylases can regulate expression of genes through modulation of the level of CD-CUTs. Analysis of binding of the transcriptional activator Zap1p and insertion of transcriptional terminators upstream from the Zap1p binding sites show that CD-CUT transcription or accumulation also interferes with binding of the transcriptional activator Zap1p. Consistent with this model, overexpressing Zap1p or using a constitutively active version of the Aft1p transcriptional activator rescues the induction defect of ZRT1 and FIT3 in NMD mutants. These results show that cryptic upstream sense transcription resulting in unstable transcripts degraded by NMD controls repression of a large number of genes located in subtelomeric regions, and in particular of many metal homeostasis genes.