Comprehensive Monogenic Diabetes Panel

28 gene panel that includes assessment of non-coding variants

Ideal for patients with a clinical suspicion of monogenic diabetes or neonatal diabetes mellitus. This comprehensive panel includes genes from the MODY Panel.

Analysis methods Availability Number of genes Test code CPT codes
PLUS
SEQ
DEL/DUP
4 weeks 28 GHC0051 SEQ 81405
SEQ 81406
SEQ 81407
DEL/DUP 81479

Summary

ICD codes
Commonly used ICD-10 code(s) when ordering the Comprehensive Monogenic Diabetes Panel

ICD-10 Disease
P70.2 Neonatal diabetes mellitus

Sample requirements:

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection. Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

About

Monogenic diabetes consists of a heterogenous group of diabetes types that are caused by mutations in single genes, estimated to represent as much as 1-2% of all cases of diabetes mellitus (DM). The main phenotypes suggestive of an underlying monogenic cause include neonatal diabetes mellitus (NDM), maturity-onset diabetes of the young (MODY) and other very rare diabetes-associated syndromes. Permanent neonatal diabetes mellitus (PNDM) is a monogenic form of neonatal diabetes characterized by persistent hyperglycemia within the first 12 months of life in general (median age of onset of nine weeks), requiring continuous insulin treatment. Initial clinical manifestations include hyperglycemia, glycosuria, intrauterine growth retardation, osmotic polyuria, severe dehydration, and failure to gain weight. The transient form of neonatal diabetes mellitus (TNDM) typically resolves by 18 months of age. Many patients display some degree of developmental coordination disorder. The incidence of NDM is estimated to be 1:95,000 to 1:150,000 live births. About 50% of NDM cases are permanent (PNDM) and 50% transient (TNDM). The condition has been reported in all ethnic groups and affects male and female infants equally. Neonatal diabetes is most commonly caused by mutations in the KCNJ11 (34%), ABCC8(24%), INS (13%) and GCK (4%) genes. The clinical manifestations differ depending on the underlying genetic defect. In KCNJ11 and ABCC8-related cases, patients usually present before three months of age with symptomatic hyperglycemia, and often ketoacidosis. Approximately 25% of patients with mutations in the KCNJ11 gene have related neurological findings, including developmental delay and epilepsy (DEND syndrome) or a milder form of DEND without seizures and with less severe developmental delay (intermediate DEND). In INS-related cases, patients present with marked hyperglycemia or diabetic ketoacidosis on average at nine weeks, but some at a much later age. GCK-related PNDM patients have permanent insulin-dependent diabetes from the first day of life. The Comprehesive Monogenic Diabetes Panel covers MODY, which is described in detail at MODY Panel description.

Panel Content

Genes in the Comprehensive Monogenic Diabetes Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ABCC8Hyperinsulinemic hypoglycemia, Diabetes, permanent neonatal, Hypoglycemia, leucine-induced, Diabetes mellitus, transient neonatalAD/AR128621
BLKMaturity onset diabetes of the youngAD57
EIF2AK3SED, Wolcott-Rallison typeAR978
FOXP3Immunodysregulation, polyendocrinopathy, and enteropathyXL2581
GATA6Heart defects, congenital, and other congenital anomalies, Atrial septal defect 9, atrioventricular septal defect 5, Persistent truncus arteriosus, Tetralogy of FallotAD1679
GCKHyperinsulinemic hypoglycemia, familial, Diabetes mellitus, permanent neonatal, Maturity-onset diabetes of the young, type 2AD/AR179825
GLIS3Diabetes mellitus, neonatal, with congenital hypothyroidismAR718
GLUD1Hyperammonemia-hyperinsulinism, Hyperinsulinemic hypoglycemiaAD/AR1438
HADH3-hydroxyacyl-CoA dehydrogenase deficiencyAR1026
HNF1AMaturity onset diabetes of the young, Renal cell carcinoma, nonpapillary clear cell, Liver adenomatosisAD72524
HNF1BRenal cell carcinoma, nonpapillary chromophobe, Renal cysts and diabetes syndromeAD34227
HNF4ACongenital hyperinsulinism, diazoxide-responsive, Maturity onset diabetes of the young, Fanconi renotubular syndrome 4 with maturity-onset diabetes of the youngAD30147
INSDiabetes mellitus, permanent neonatal, Hyperproinsulinemia, familial, with or without diabetes, Maturity onset diabetes of the youngAD3376
INSRHyperinsulinemic hypoglycemia, familial, Rabson-Mendenhall syndrome, Donohoe syndromeAD/AR44183
KCNJ11Hyperinsulinemic hypoglycemia, Diabetes, permanent neonatal, Diabetes mellitus, transient neonatal, Maturity-onset diabetes of the young 13, Paternally-inherited mutations can cause Focal adenomatous hyperplasiaAD/AR56173
KLF11Maturity onset diabetes of the youngAD13
NEUROD1Maturity onset diabetes of the youngAD317
NEUROG3Diarrhea, malabsorptive, congenitalAR38
PAX4Diabetes mellitusAD310
PDX1Pancreatic agenesis, Neonatal diabetes mellitus, Maturity-onset diabetes of the young, type 4, Lactic acidemia due to PDX1 deficiencyAD/AR1026
PPARGInsulin resistance, Lipodystrophy, familial, partialAD/Digenic (Severe digenic insulin resistance can be due to digenic mutations in PPP1R3A and PPARG)1948
PTF1APancreatic and cerebellar agenesis, Pancreatic agenesis 2AR415
RFX6Pancreatic hypoplasia, intestinal atresia, and gallbladder aplasia or hypoplasia, with or without tracheoesophageal fistula, Martinez-Frias syndrome, Mitchell-Riley syndromeAR1028
SLC2A2Glycogen storage disease, Fanconi-Bickel syndrome, Neonatal diabetes mellitusAR2272
SLC16A1Hyperinsulinemic hypoglycemia, familial, Erythrocyte lactate transporter defect, Monocarboxylate transporter 1 deficiency, Myoclonic-atonic epilepsyAD/AR1214
UCP2HyperinsulinismAD/AR7
WFS1Wolfram syndrome, Deafness, Wolfram-like syndrome, autosomal dominant, Deafness, autosomal dominant 6/14/38, Cataract 41AD/AR68351
ZFP57Diabetes mellitus, transient neonatal, 1AD714

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ABCC8Chr11:17498513c.-190C>GNM_000352.3
ABCC8Chr11:17465872c.1333-1013A>GNM_000352.3
BLKChr8:11422122c.*505G>TNM_001715.2
FOXP3ChrX:49106919c.*876A>GNM_014009.3
FOXP3ChrX:49106917c.*878A>GNM_014009.3
GATA6Chr18:19749272c.-409C>GNM_005257.4
GATA6Chr18:19749151c.-530A>TNM_005257.4
GCKChr7:44229109c.-557G>CNM_000162.3
HADHChr4:108945190c.636+471G>TNM_001184705.2rs786200932
HADHChr4:108948955c.709+39C>GNM_001184705.2
HNF1AChr12:121416453c.-119G>ANM_000545.5rs371945966
HNF1AChr12:121416448c.-124G>CNM_000545.5rs563304627
HNF1AChr12:121416385c.-187C>A/TNM_000545.5
HNF1AChr12:121416354c.-218T>CNM_000545.5
HNF1AChr12:121416314c.-258A>GNM_000545.5rs756136537
HNF1AChr12:121416289c.-283A>CNM_000545.5
HNF1AChr12:121416285c.-287G>ANM_000545.5
HNF1AChr12:121416281c.-291T>CNM_000545.5rs534474388
HNF1AChr12:121416110c.-462G>ANM_000545.5
HNF1AChr12:121416034c.-538G>CNM_000545.5
HNF1AChr12:121416510c.-62C>GNM_000545.5rs753567412
HNF1AChr12:121416475c.-97T>GNM_000545.5
HNF4AChr20:42984309c.-136A>GNM_175914.4
HNF4AChr20:42984299c.-146T>CNM_175914.4
HNF4AChr20:42984276c.-169C>TNM_175914.4
HNF4AChr20:42984271c.-174T>CNM_175914.4
HNF4AChr20:42984264c.-181G>ANM_175914.4
HNF4AChr20:42984253c.-192C>GNM_175914.4
HNF4AChr20:43036000c.291-21A>GNM_000457.4
INSChr11:2181023c.*59A>GNM_000207.2rs397515519
INSChr11:2181774c.187+241G>ANM_000207.2
INSChr11:2181242c.188-15G>ANM_000207.2rs574629011
INSChr11:2181258c.188-31G>ANM_000207.2rs797045623
KCNJ11Chr11:17409772c.-134G>TNM_000525.3rs387906398
KCNJ11Chr11:17409692c.-54C>TNM_000525.3
NEUROD1Chr2:182545307c.-162G>ANM_002500.4rs537184640
PTF1AChr10:23508305c.*25470A>GNM_178161.2
PTF1AChr10:23508363c.*25528A>GNM_178161.2
PTF1AChr10:23508365c.*25530A>GNM_178161.2
PTF1AChr10:23508437c.*25602A>GNM_178161.2
PTF1AChr10:23508446c.*25611A>CNM_178161.2
RFX6Chr6:117198947c.224-12A>GNM_173560.3
SLC16A1Chr1:113498814c.-202G>ANM_003051.3rs387906403
SLC16A1Chr1:113499002c.-391_-390insACGCCGGTCACGTGGCGGGGTGGGGNM_003051.3rs606231172
SLC2A2Chr3:170745041c.-582A>CNM_000340.1
WFS1Chr4:6271704c.-43G>TNM_006005.3

Panel Update

Genes added

  • GATA6
  • PTF1A
  • RFX6
  • ZFP57

Genes removed

  • G6PC2

Test strength and Limitations

The strengths of this test include:

  • CAP and ISO-15189 accreditations covering all operations at GHC Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in GHC WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: *PPA2* (11, 12). Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:
  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than GHC Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

Test Performance

The GHC Genetics panel covers classical genes associated with Brugada syndrome, catecholaminergic polymorphic ventricular tachycardia (CPVT), cardiac arrest underlying cardiac condition, cardiac arrest cause unspecified, syncope and collapse, abnormal ECG, Long QT syndrome, arrhythmogenic right ventricular cardiomyopathy (ARVC) and Short QT syndrome. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. GHC Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient’s phenotype is suggestive of a specific mutation type.

Performance of GHC Genetics Whole Exome Sequencing (WES) assay.
All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
The performance presented above reached by WES with the following coverage metrics
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Detection of Del/Dup of several genes is by MLPA analysis (MS Holland). All genes are performed by CNV analysis through the genome depending on exon size, sequencing coverage and sequence content. We have validated the assays for different starting materials including isolated DNA from EDTA blood that provide high-quality results.

Bioinformatics & clinical interpretation

The sequencing data generated in our laboratory is analysed by our bioinformatic pipeline, integrating state-of-the art algorithms and industry-standard software solutions. We use also JSI medical systems software for sequencing data analysis. JSI medical systems is a certified system offering sophisticated bioinformatic software solutions covering a wide field of sequencing techniques.

Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results.

Every pathogenic or probably pathogenic variant is confirmed by the Sanger sequencing method. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. The analysis of detected variants was performed on the basis of the reference database of polymorphisms and international mutation databases: UMD, LOVD and ClinVar.

The consequence of variants in coding and splice regions are estimated using Alamut software. The Alamut database contains more than 28000 coding genes, non-protein coding genes and pseudogenes. This database (shared with the high throughput annotation engine for NGS data, Alamut Batch) is frequently updated. Information comes from different public databases such as NCBI, EBI, and UCSC, as well as other sources including gnomAD, ESP, Cosmic, ClinVar, or HGMD and CentoMD (for those a separate subscription from Qiagen/Biobase and Centogene respectively is required). Alamut Visual finds information about nucleotide conservation data through many vertebrates’ species, with the phastCons and phyloP scores, amino acid conservation data through orthologue alignments and information on protein domains.

Moreover, we integrate several missense variant pathogenicity prediction tools and algorithms such as SIFT, PolyPhen, AlignGVGD or MutationTaster. It also offers a window dedicated to the in silico study of variants’ effect on RNA splicing, allowing the assessment of their potential impact on splice junctions and visualization of cryptic or de novo splice sites. Impact on splicing regulation is also assessed.


Clinical interpretation

At GHC Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical report. We recommend an interpretation of the findings of this molecular genetic analysis, including subsequent oncological consultation for the patient in the context of genetic counselling for the patient.

We strive to continuously monitor current genetic literature identifying new relevant information and findings and adapting them to our diagnostics. This enables relevant novel discoveries to be rapidly translated and adopted into our ongoing diagnostics development without delay. The undertaking of such comprehensive due diligence ensures that our diagnostic panels and clinical statements are the most up-to-date on the market.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analysed at our laboratories enables us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant three times at GHC Genetics. Reported variants of uncertain significance (VUS) are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size >10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at GHC Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counselling.

Our Clinical interpretation team analyses millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratories are therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by GHC Genetics is re-classified, our laboratories will issue a follow-up statement to the original ordering health care provider at no additional cost.