Microcephaly and Pontocerebellar Hypoplasia Panel

Updated
Summary
  • Is a 78 gene panel that includes assessment of non-coding variants.
  • Is ideal for patients with a clinical suspicion of microcephaly or pontocerebellar hypoplasias.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

78

Test code

MA0701

Panel size

Large

CPT code *
81443(1)
* The CPT codes provided are based on AMA guidelines and are for informational purposes only. CPT coding is the sole responsibility of the billing party. Please direct any questions regarding coding to the payer being billed.

Summary

The Blueprint Genetics Microcephaly and Pontocerebellar Hypoplasia Panel (test code MA0701):

ICD codes

Commonly used ICD-10 code(s) when ordering the Microcephaly and Pontocerebellar Hypoplasia Panel

ICD-10 Disease
Q02 Microcephaly
Q04.3 Pontocerebellar hypoplasias

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Please see Sample Requirements for accepted saliva kits)

Label the sample tube with your patient's name, date of birth and the date of sample collection.

We do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. In addition, if the patient is affected with a hematological malignancy, DNA extracted from a non-hematological source (e.g. skin fibroblasts) is strongly recommended.

Please note that, in rare cases, mitochondrial genome (mtDNA) variants may not be detectable in blood or saliva in which case DNA extracted from post-mitotic tissue such as skeletal muscle may be a better option.

Read more about our sample requirements here.

Microcephaly is a neurodevelopmental disorder. It is usually defined as a head circumference (HC) more than two (or three) standard deviations below the mean for age and sex and serves as an important neurological indication or warning sign, however uniformity in its definition is lacking. Microcephaly may be congenital or develop in the first few years of life. In general, life expectancy for individuals with microcephaly is reduced and the prognosis for normal brain function is poor. It may stem from a wide variety of conditions that cause abnormal growth of the brain, or from syndromes associated with chromosomal abnormalities. A homozygous mutation in one of the microcephalin genes (MCPH1, ASPM, WDR62) causes primary microcephaly. Najm type X-linked intellectual deficit (point mutations and deletions in the CASK gene) is a rare cerebellar dysgenesis syndrome associated with microcephaly in most cases. Examples of monogenic syndromes associated with microcephaly are Seckel syndrome spectrum disorders. Nonsyndromic pontocerebellar hypoplasias (PCH) are a rare heterogeneous group of diseases characterized by hypoplasia and atrophy and/or early neurodegeneration of the cerebellum and pons. PCH patients of all subtypes present with progressive microencephaly, delayed or absence of cognitive and voluntary motor development, intellectual deficit, spasticity, chorea/dyskinesia, swallowing difficulties and seizures. The majority of PCH cases are caused by mutations in tRNA splicing endonuclease (TSEN genes). Approximately half the cases of PCH subtype 1 are due to mutations in the EXOSC3 gene. Other subtypes include mutations in for example TSEN2 and TSEN54 genes. Diagnosis is made based on clinical symptoms and neuroradiological findings (MRI) and can be confirmed by molecular genetic analyses. Nonsyndromic pontocerebellar hypoplasias (PCH) are generally inherited in an autosomal recessive pattern. Isolated microcephaly is known to have autosomal dominant, autosomal recessive and X-linked inheritance.

Genes in the Microcephaly and Pontocerebellar Hypoplasia Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
AKT3 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome AD 13 28
AMPD2 Pontocerebellar hypoplasia type 9, Spastic paraplegia 63 AR 14 18
ASPM Microcephaly AR 176 212
ASXL1 Bohring-Opitz syndrome AD 41 39
ASXL3 Bainbridge-Ropers syndrome AD 45 49
ATR Cutaneous telangiectasia and cancer syndrome, Seckel syndrome AD/AR 10 33
CASK Mental retardation and microcephaly with pontine and cerebellar hypoplasia, FG syndrome, Mental retardation XL 87 112
CCDC47 Microcephaly, Malformations AR 1
CDK5RAP2 Microcephaly AR 19 21
CENPF Ciliary dyskinesia -Lethal Ciliopathy AR 13 8
CENPJ Seckel syndrome, Microcephaly AR 34 9
CEP152 Seckel syndrome, Microcephaly AR 20 20
CEP63 Seckel syndrome AR 7 2
CSNK2A1 Jeune asphyxiating thoracic dystrophy, Joubert syndrome 21 14 20
DONSON Microcephaly, short stature, and limb abnormalities (MISSLA), Microcephaly-Micromelia syndrome 10 19
DYNC1H1 Spinal muscular atrophy, Charcot-Marie-Tooth disease, Mental retardation AD 60 71
DYRK1A Mental retardation AD 94 77
EFTUD2 Mandibulofacial dysostosis with microcephaly, Esophageal atresia, syndromic AD 45 99
EXOSC3 Pontocerebellar hypoplasia AR 11 19
GFM1 Combined oxidative phosphorylation deficiency AR 19 19
GPT2 Mental retardation, autosomal recessive 49, Microcephaly, Spastic paraplegia AR 5 7
KANSL1* Koolen-de Vries syndrome AD 61 64
KATNB1 Lissencephaly 6, with microcephaly AR 6 10
KIF11 Microcephaly AD 39 69
LIG4 Severe combined immunodeficiency with sensitivity to ionizing radiation, LIG4 syndrome AR 18 36
MBD5 Mental retardation AD 62 90
MCPH1# Microcephaly AR 23 32
MED17 Microcephaly, postnatal progressive, with seizures and brain atrophy AR 4 4
MFSD2A Microcephaly 15, primary, autosomal recessive AR 4 4
MIPEP* Combined oxidative phosphorylation deficiency 31 AR 5 8
MRE11A Ataxia-telangiectasia-like disorder-1 AR 57 56
MYCN Feingold syndrome AD 27 41
MYO18B Klippel-Feil syndrome 4, autosomal recessive, with myopathy and facial dysmorphism AR 2 4
NCAPD3 Microcephaly AR 3 5
NDE1 Microhydranencephaly, Lissencephaly AR 13 18
NHEJ1 Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation AR 15 16
OPHN1 Mental retardation, with cerebellar hypoplasia and distinctive facial appearance XL 28 42
PAFAH1B1 Lissencephaly, Subcortical laminar heterotopia AD 121 169
PCDH12 Microcephaly AR 1 6
PCLO Pontocerebellar hypoplasia AR 1 2
PCNT Microcephalic osteodysplastic primordial dwarfism AR 49 88
PHGDH Neu-Laxova syndrome 1 AR 13 23
PLK4 Microcephaly and chorioretinopathy, autosomal recessive 2 AR 3 6
PNKP Epileptic encephalopathy, early infantile, Ataxia-oculomotor AR 34 23
POMT1 Muscular dystrophy-dystroglycanopathy AR 47 96
PQBP1 Renpenning syndrome XL 14 18
QARS Microcephaly, progressive, seizures, and cerebral and cerebellar atrophy AR 14 10
RARS2 Pontocerebellar hypoplasia AR 23 37
RTTN Microcephaly, short stature, and polymicrogyria with or without seizures AR 16 16
SEPSECS Pontocerebellar hypoplasia, type 2D AR 10 15
SLC1A4 Spastic tetraplegia, thin corpus callosum, and progressive microcephaly AR 4 8
SMARCA2 Nicolaides-Baraitser syndrome AD 41 73
SMARCE1 Coffin-Siris syndrome AD 14 12
SOX11 Mental retardation, autosomal dominant 27 AD 11 14
STAG2 Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder XL 6 14
STAMBP Microcephaly-capillary malformation syndrome AR 15 19
STIL Microcephaly AR 13 17
TBC1D20 Warburg micro syndrome 4 AR 6 6
TBC1D23 Pontocerebellar hypoplasia, type 11 5 9
THOC6 Microcephaly AR 8 9
TMTC3 Lissencephaly 8 6 10
TOE1 Pontocerebellar hypoplasia type 7 11 12
TOP3A 8
TRMT10A Microcephaly, short stature, and impaired glucose metabolism 1 AR 2 7
TSEN2# Pontocerebellar hypoplasia AR 8 5
TSEN54 Pontocerebellar hypoplasia AR 23 21
TUBB* Congenital symmetric circumferential skin creases 1, Cortical dysplasia, complex, with other brain malformations 6 AD 11 7
TUBB2B#* Polymicrogyria, asymmetric AD 21 30
TUBGCP4 Microcephaly and chorioretinopathy, autosomal recessive 3 AR 7 6
TUBGCP6 Microcephaly and chorioretinopathy, autosomal recessive 1 AR 16 7
UBE3B Blepharophimosis-Ptosis-Intellectual-Disability syndrome (Kaufman oculocerebrofacial syndrome) AR 14 24
VARS Early-onset progressive encephalopathy with brain atrophy and thin corpus callosum (PEBAT), Encephalopathy, progressive AR 12 6
VRK1 Pontocerebellar hypoplasia AR 9 9
WDR62 Microcephaly AR 33 48
WDR73 Galloway-Mowat syndrome AR 9 12
XRCC4 Short stature, microcephaly, and endocrine dysfunction AR 9 10
ZNF148 Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies (GDACCF) 5 4
ZNF335 Microcephaly 10, primary, autosomal recessive AR 8 12

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence reads.

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), mitochondrial (mi), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Mitomap databases.

Non-coding variants covered by Microcephaly and Pontocerebellar Hypoplasia Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ASPM Chr1:197097820 c.2761-25A>G NM_018136.4 rs199422149
CDK5RAP2 Chr9:123182253 c.4005-15A>G NM_018249.5 rs387906274
CEP152 Chr15:49059406 c.2148-17G>A NM_001194998.1 rs751691427
DONSON Chr21:34955994 c.786-22A>G NM_017613.3 rs1135401960
EXOSC3 Chr9:37782146 c.475-12A>G NM_016042.3 rs370087266
NCAPD3 Chr11:134086816 c.382+14A>G NM_015261.2
PNKP Chr19:50364799 c.1387-33_1386+49delCCTCCTCCCCTGACCCC NM_007254.3 rs752902474
POMT1 Chr9:134379574 c.-30-2A>G NM_007171.3
RARS2 Chr6:88244587 c.613-3927C>T NM_020320.3
RTTN Chr18:67727297 c.4748-19T>A NM_173630.3
RTTN Chr18:67815044 c.2309+1093G>A NM_173630.3
STAMBP Chr2:74077998 c.1005+358A>G NM_006463.4
XRCC4 Chr5:82400728 c.-10-1G>T NM_022406.2 rs869320678

Test Strengths

The strengths of this test include:
  • CAP accredited laboratory
  • 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
  • Some of the panels include the whole mitochondrial genome (please see the Panel Content section)
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publicly available analytic validation demonstrating complete details of test performance
  • ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
  • Our rigorous 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: MCPH1 (NM_001322042:14), TSEN2 (NM_001321278:12). Genes with suboptimal coverage in our assay are marked with number sign (#) and 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. Gene is considered to have suboptimal coverage when >90% of the gene's target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. 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
  • Some of the panels include the whole mitochondrial genome but not all (please see the Panel Content section)
  • 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 in nuclear genes (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Low level heteroplasmy in mtDNA (>90% are detected at 5% level)
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments
  • Some disease causing variants present in mtDNA are not detectable from blood, thus post-mitotic tissue such as skeletal muscle may be required for establishing molecular diagnosis.

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

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

The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).

Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999%
Insertions, deletions and indels by sequence analysis
1-10 bps 99.2% (7,745/7,806) >99.9999%
11-50 bps 99.13% (2,524/2,546) >99.9999%
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (25/25)
     
The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics
     
Mean sequencing depth 143X
Nucleotides with >20x sequencing coverage (%) 99.86%


Performance of Blueprint Genetics Mitochondrial Sequencing Assay.

Sensitivity % Specificity %
ANALYTIC VALIDATION (NA samples; n=4)
Single nucleotide variants
Heteroplasmic (45-100%) 100.0% (50/50) 100.0%
Heteroplasmic (35-45%) 100.0% (87/87) 100.0%
Heteroplasmic (25-35%) 100.0% (73/73) 100.0%
Heteroplasmic (15-25%) 100.0% (77/77) 100.0%
Heteroplasmic (10-15%) 100.0% (74/74) 100.0%
Heteroplasmic (5-10%) 100.0% (3/3) 100.0%
Heteroplasmic (<5%) 50.0% (2/4) 100.0%
CLINICAL VALIDATION (n=76 samples)
All types
Single nucleotide variants n=2026 SNVs
Heteroplasmic (45-100%) 100.0% (1940/1940) 100.0%
Heteroplasmic (35-45%) 100.0% (4/4) 100.0%
Heteroplasmic (25-35%) 100.0% (3/3) 100.0%
Heteroplasmic (15-25%) 100.0% (3/3) 100.0%
Heteroplasmic (10-15%) 100.0% (9/9) 100.0%
Heteroplasmic (5-10%) 92.3% (12/13) 99.98%
Heteroplasmic (<5%) 88.9% (48/54) 99.93%
Insertions and deletions by sequence analysis n=40 indels
Heteroplasmic (45-100%) 1-10bp 100.0% (32/32) 100.0%
Heteroplasmic (5-45%) 1-10bp 100.0% (3/3) 100.0%
Heteroplasmic (<5%) 1-10bp 100.0% (5/5) 99,997%
SIMULATION DATA /(mitomap mutations)
Insertions, and deletions 1-24 bps by sequence analysis; n=17
Homoplasmic (100%) 1-24bp 100.0% (17/17) 99.98%
Heteroplasmic (50%) 100.0% (17/17) 99.99%
Heteroplasmic (25%) 100.0% (17/17) 100.0%
Heteroplasmic (20%) 100.0% (17/17) 100.0%
Heteroplasmic (15%) 100.0% (17/17) 100.0%
Heteroplasmic (10%) 94.1% (16/17) 100.0%
Heteroplasmic (5%) 94.1% (16/17) 100.0%
Copy number variants (separate artifical mutations; n=1500)
Homoplasmic (100%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (50%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (30%) 500 bp, 1kb, 5 kb 100.0% 100.0%
Heteroplasmic (20%) 500 bp, 1kb, 5 kb 99.7% 100.0%
Heteroplasmic (10%) 500 bp, 1kb, 5 kb 99.0% 100.0%
The performance presented above reached by following coverage metrics at assay level (n=66)
Mean of medians Median of medians
Mean sequencing depth MQ0 (clinical) 18224X 17366X
Nucleotides with >1000x MQ0 sequencing coverage (%) (clinical) 100%
rho zero cell line (=no mtDNA), mean sequencing depth 12X

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. If the test includes the mitochondrial genome the target region gene list contains the mitochondrial genes. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as  SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with suboptimal coverage (<20X for nuclear genes and <1000X for mtDNA) if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the ACMG guideline 2015.

The final step in the analysis is orthogonal confirmation. Sequence and copy number variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing by orthogonal methods such as qPCR/ddPCR when they do not meet our stringent NGS quality metrics for a true positive call.

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, abstracts and variant databases used to help ordering providers 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. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.

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