Abnormal Genitalia/ Disorders of Sex Development Panel

Updated
Summary
  • Is a 62 gene panel that includes assessment of non-coding variants.
  • Is ideal for patients presenting with ambiguous genitalia, patients suspected to have a disorder of sexual development and patients suspected to have congenital adrenal hyperplasia (CAH).

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

62

Test code

EN0201

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 Abnormal Genitalia/ Disorders of Sex Development Panel (test code EN0201):

ICD codes

Commonly used ICD-10 code(s) when ordering the Abnormal Genitalia/ Disorders of Sex Development Panel

ICD-10 Disease
Q56.0 Indeterminate sex and pseudohermaphroditism
Q56.1 Male pseudohermaphroditism
Q56.2 Female pseudohermaphroditism
E34.50 Androgen insensitivity syndrome
Q55.8 Persistent Mullerian duct syndrome
E25.0 Congenital adrenal hyperplasia

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.

Disorders of sex development (DSD) are a group of congenital conditions characterized by problems in the course of gender patterning, gonadal and sex development. It has been estimated that 1% – 2% of live births have some aspect of DSD. Approximately 5% of infants with DSD have ambiguous genitalia and indeterminate sex at birth. However, the vast majority of these patients do not require corrective surgery. Patients with 46,XY DSD have often impaired androgen synthesis or action and may have normal female external genitalia, while patients with 46,XX DSD conditions have often androgen excess. In 46,XX females, congenital adrenal hyperplasia (CAH) caused by 21-hydroxylase deficiency (21-OHD) is the most common cause of DSD. The estimated prevalence of CAH is 1:10,000 and 90%-95% of cases are due to mutations in CYP21A2. The severity of the condition often depends on the residual enzyme activity subdiving CYP21A2 mutations in severe (classic phenotype, enzyme activity 0%-10%) and mild (non-classic, enzyme activity 20%-50%). Androgen insensitivity syndrome (AIS), caused by mutations in AR, is characterized by feminization of external genitalia and atypical sexual development in 46,XY individuals. The condition may be complete, partial or mild, depending on the level of androgen insensitivity. Mutations in the AR gene explain up to 95% of cases with complete androgen insensitivity, while the proportions are lower for the partial and mild subtypes. The combined prevalence of various AIS subtypes is estimated to be 5:100,000.

Genes in the Abnormal Genitalia/ Disorders of Sex Development Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
AMH Persistent Mullerian duct syndrome AR 5 56
AMHR2 Persistent Mullerian duct syndrome AR 6 37
ANOS1* Kallmann syndrome XL/Digenic 36 186
AR Androgen insensitivity, Spinal and bulbar muscular atrophy, X-linked 1, Hypospadias 1, X-linked XL 147 612
ARX# Lissencephaly, Epileptic encephalopathy, Corpus callosum, agenesis of, with abnormal genitalia, Partington syndrome, Proud syndrome, Hydranencephaly with abnormal genitalia, Mental retardation XL 66 93
ATRX Carpenter-Waziri syndrome, Alpha-thalassemia/mental retardation syndrome, Holmes-Gang syndrome, Juberg-Marsidi syndrome, Smith-Fineman-Myers syndrome, Mental retardation-hypotonic facies syndrome XL 65 165
BCOR Microphthalmia, syndromic, Oculofaciocardiodental syndrome XL 40 53
CDK9 AR 1
CDKN1C Beckwith-Wiedemann syndrome, IMAGE syndrome AD 35 81
CEP41 Joubert syndrome AR/Digenic 7 11
CHD7 Isolated gonadotropin-releasing hormone deficiency, CHARGE syndrome AD 276 860
CREBBP Rubinstein-Taybi syndrome AD 175 362
CYB5A 46, XY disorder of sex development, Methemoglobinemia, type IV AR 3 5
CYP11A1 Adrenal insufficiency, congenital, with 46,XY sex reversal, partial or complete AD/AR 14 28
CYP11B1* Adrenal hyperplasia, congenital, due to 11-beta-hydroxylase deficiency, Glucocorticoid-remediable aldosteronism AD/AR 55 147
CYP17A1 Adrenal hyperplasia, congenital, due to 17-alpha-hydroxylase deficiency AR 35 126
CYP19A1 Aromatase deficiency, Aromatase excess syndrome AR 17 52
CYP21A2* Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency, Hyperandrogenism, nonclassic , due to 21-hydroxylase deficiency AR 48 296
DHCR7 Smith-Lemli-Opitz syndrome AR 88 217
DHH 46,XY partial gonadal dysgenesis, with minifascicular neuropathy, 46,XY sex reversal 7 AD/AR 5 18
DYNC2H1 Short -rib thoracic dysplasia with or without polydactyly type 1, Short -rib thoracic dysplasia with or without polydactyly type 3, Asphyxiating thoracic dysplasia (ATD; Jeune), SRPS type 2 (Majewski) AR/Digenic 148 205
ERCC3 Xeroderma pigmentosum, Trichothiodystrophy, photosensitive AR 10 19
FEZF1 Hypogonadotropic hypogonadism 22 with or without anosmia, Kallmann syndrome AR 2 3
FGF8 Hypogonadotropic hypogonadism AD/Digenic 18 36
FGFR1 Pfeiffer syndrome, Trigonocephaly, Hypogonadotropic hypogonadism, Osteoglophonic Dwarfism - Craniostenosis, Hartsfield syndrome AD/Digenic/Multigenic 72 257
FIG4 Amyotrophic lateral sclerosis, Polymicrogyria, bilateral occipital, Yunis-Varon syndrome, Charcot-Marie-Tooth disease AD/AR 34 69
FRAS1 Fraser syndrome AR 27 58
GATA4* Tetralogy of Fallot, Atrioventricular septal defect, Testicular anomalies with or without congenital heart disease, Ventricular septal defect, Atrial septal defect AD 37 140
GNRH1 Hypogonadotropic hypogonadism 12 with or without anosmia AR/Digenic 1 10
GNRHR Hypogonadotropic hypogonadism AD/AR/Digenic 23 58
HSD17B3 17-Beta hydroxysteroid dehydrogenase III deficiency AR 24 63
HSD3B2 3-beta-hydroxysteroid dehydrogenase, II deficiency AR 11 63
IL17RD Hypogonadotropic hypogonadism AD/Digenic 6 10
IRF6 Orofacial cleft, Popliteal pterygium syndrome, van der Woude syndrome AD 45 338
KISS1 Hypogonadotropic hypogonadism 13 with or without anosmia, Central precocious puberty AR 1 10
KISS1R Precocious puberty, central 1 AD/AR 7 36
LHB* Hypogonadotropic hypogonadism 23 with or without anosmia AR 6 8
LHCGR Precocious puberty, male, Leydig cell hypoplasia, Luteinizing hormone resistance, female AR 34 76
MAMLD1 Hypospadias 2, X-linked XL 5 20
MAP3K1 46,XY sex reversal 6 AD 9 27
MKRN3 Central precocious puberty AD 6 32
MKS1 Bardet-Biedl syndrome, Meckel syndrome AR 50 52
NR0B1 Adrenal hypoplasia, congenital, 46,XY sex reversal XL 73 252
NR5A1 Adrenocortical insufficiency, Premature ovarian failure, 46,XY sex reversal AD/AR 28 183
POR Disordered steroidogenesis due to cytochrome p450 oxidoreductase deficiency, Antley-Bixler syndrome AR 14 70
PROK2 Hypogonadism, hypogonadotropic, Kallmann syndrome AD/AR 7 20
PROKR2 Hypogonadotropic hypogonadism AD/AR 9 54
RSPO1 Palmoplantar hyperkeratosis with squamous cell carcinoma of skin and 46,XX sex reversal AR 3 5
SAMD9 Mirage syndrome, Tumoral calcinosis, normophosphatemic AD/AR 10 27
SGPL1 Nephrotic syndrome 14 AR 8 17
SOX10 Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease, Kallmann syndrome AD 56 148
SOX9 Campomelic dysplasia, 46,XY sex reversal, Brachydactyly with anonychia (Cooks syndrome) AD 47 144
SRD5A2 Steroid 5-alpha-reductase 2 deficiency AR 45 119
SRY 46,XX disorder of sex development, 46,XY disorder of sex development YL 29 109
STAR Lipoid adrenal hyperplasia AR 34 83
TAC3 Hypogonadotropic hypogonadism AR 5 10
TACR3 Hypogonadotropic hypogonadism AR 8 36
TOE1 Pontocerebellar hypoplasia type 7 11 12
TSPYL1 Sudden infant death with dysgenesis of the testes syndrome, 46, XY disorder of sex development AR 1 8
WDR11 Hypogonadotropic hypogonadism, Kallmann syndrome AD 3 17
WT1 Denys-Drash syndrome, Frasier syndrome, Wilms tumor, Nephrotic syndrome, type 4 AD 42 183
ZFPM2 46,XY sex reversal, Diaphragmatic hernia 3, Tetralogy of Fallot AD/AR 9 50

* 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 Abnormal Genitalia/ Disorders of Sex Development Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
AMH Chr19:2249105 NM_000479.3
AMHR2 Chr12:53819422 c.622-51C>T NM_020547.2
AMHR2 Chr12:53819426 c.622-47C>T NM_020547.2 rs200782636
AR ChrX:66764442 c.-547C>T NM_000044.3
AR ChrX:66788676 c.1616+22072A>C NM_000044.3
AR ChrX:66905841 c.1769-11T>A NM_000044.3
AR ChrX:66942551 c.2450-118A>G NM_000044.3
AR ChrX:66942627 c.2450-42G>A NM_000044.3
CDKN1C Chr11:2905209 c.*5+20G>T NM_000076.2 rs760540648
CHD7 Chr8:61734568 c.2836-15C>G NM_017780.3
CHD7 Chr8:61757794 c.5051-15T>A NM_017780.3
CHD7 Chr8:61763034 c.5405-18C>A NM_017780.3 rs199981784
CHD7 Chr8:61763035 c.5405-17G>A NM_017780.3 rs794727423
CHD7 Chr8:61763039 c.5405-13G>A NM_017780.3 rs1131690787
CREBBP Chr16:3788684 c.4281-11C>G NM_004380.2 rs587783493
CYP11B1 Chr8:143958423 c.595+16G>T NM_000497.3
CYP21A2 Chr6:32006858 c.293-13C>G NM_000500.7 rs6467
DYNC2H1 Chr11:103019205 c.2819-14A>G NM_001080463.1 rs781091611
DYNC2H1 Chr11:103055609 c.6478-16G>A NM_001080463.1 rs376892534
GATA4 Chr8:11561282 c.-989C>T NM_002052.3
GATA4 Chr8:11561369 c.-902G>T NM_002052.3
GATA4 Chr8:11561399 NM_002052.3 rs1195641788
GATA4 Chr8:11612500 c.910-55T>C NM_002052.3
GATA4 Chr8:11612745 c.997+103G>T NM_002052.3 rs113049875
GATA4 Chr8:11614418 c.998-26G>A NM_002052.3
IRF6 Chr1:209975332 c.-19C>A NM_006147.3
IRF6 Chr1:209975361 c.-48A>T NM_006147.3
IRF6 Chr1:209979367 c.-151G>A NM_006147.3
IRF6 Chr1:209979435 c.-219C>T NM_006147.3
IRF6 Chr1:209989478 c.-10263dupT NM_006147.3
KISS1 Chr1:204165663 c.-198C>T NM_002256.3 rs770004886
MKRN3 Chr15:23810776 c.-150_-147delTCAG NM_005664.3
MKRN3 Chr15:23810849 c.-81C>T NM_005664.3
POR Chr7:75544501 c.-5+4A>G NM_000941.2
SOX10 Chr22:38379877 c.-84-2A>T NM_006941.3
SOX10 Chr22:38412215 c.-31954C>T NM_006941.3 rs606231342
SOX10 Chr22:38412781 c.-32520C>G NM_006941.3 rs533778281
SOX9 Chr17:70117348 c.-185G>A NM_000346.3
SRY ChrY:2655719 c.-75G>A NM_003140.2
SRY ChrY:2655774 c.-133_-131delAGG NM_003140.2
SRY ChrY:2655774 c.-130G>C NM_003140.2
STAR Chr8:38003676 c.466-11T>A NM_000349.2

Added and removed genes from the panel

Genes added Genes removed
MT-ATP6
MT-ATP8
MT-CO1
MT-CO2
MT-CO3
MT-CYB
MT-ND1
MT-ND2
MT-ND3
MT-ND4
MT-ND4L
MT-ND5
MT-ND6
MT-RNR1
MT-RNR2
MT-TA
MT-TC
MT-TD
MT-TE
MT-TF
MT-TG
MT-TH
MT-TI
MT-TK
MT-TL1
MT-TL2
MT-TM
MT-TN
MT-TP
MT-TQ
MT-TR
MT-TS1
MT-TS2
MT-TT
MT-TV
MT-TW
MT-TY

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

A significant proportion of pathogenic CYP21A2 variants are secondary to gene conversions.  We have been able to detect some gene conversions and some copy number variants in patients referred to clinical testing; however, we have not performed an analytic validation of these variant types and our detection capabilities are likely limited.
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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