Genetic Testing for Genetic Conditions

Next Generation Sequencing for the most accurate and comprehensive picture of your child’s genetic health!

Our Test Approach

Using Next-generation sequencing (NGS), Baby Genes performs full exon sequencing of targeted genes +/- ­25bp into the flanking intronic regions to identify potential variants. Results are analyzed and interpreted by the Baby Genes laboratory and medical staff. The clinical report delivers information on any pathogenic or likely pathogenic variants and their clinical significance. For carrier testing, variants of unknown significance (VUS) are not reported. For supplemental newborn and reflex testing, VUS and additional findings (e.g., psuedo-deficiency alleles) are reported to provide complete information.

 

Methodology

NGS: Nucleic acid from the submitted specimen is enriched for coding and adjacent noncoding regions of the genes on the panel using a custom capture kit (ArcherDx, Boulder, CO). The library products were sequenced with 2 by 150 bp reads on either the Illumina Miseq or NextSeq sequencing instruments (Illumina, San Diego, CA). After alignment to the reference genome (hg19), off target, low quality and duplicate reads are removed and variants are detected with the variant calling algorithms in the software listed below. This test detects single nucleotide substitutions (SNVs), small insertions and deletions, and copy number variations located in the DNA coding sequences and known splice regions in the genes targeted by the panel. All sequence alterations are described according to the Human Genome Variation Society (HGVS) nomenclature guidelines and are classified according to the guidelines for sequence variant interpretation of the American College of Medical Genetics and Genomics (ACMG). Variant classification categories include pathogenic, likely pathogenic, variant of unknown significance (VUS), likely benign, and benign with VUS, likely benign and benign variants excluded from the report.

Spinal Muscular Atrophy (SMA): SMA status is assessed via copy number analysis using the data generated via the NGS panel described above. Normalized coverage of exons 7-8 are compared against healthy cohort data to determine copy status. SMN1 specific primers are part of the NGS panel and are used to detect the silent allele polymorphism (g.27134T>G).

Fragile X: A PCR-based assay is used to determine the size of the CGG repeat region of FMR1. The reported number of repeats is estimated to be accurate within two repeats for the normal and intermediate ranges and five repeats for the premutation to full mutation.

 

Genes & Diseases

GeneCytogenic LocationPrimary ConditionNewbornCarrier
ABCD1Xq28X-linked adrenoleukodystrophy
  • ABCD414q24.3Methylmalonic acidemia
  • ACAD811q25Isobutyryl-CoA dehydrogenase (IBD) deficiency
  • ACADM1p31Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency
  • ACADS12q24.31Short-chain acyl-CoA dehydrogenase (SCAD) deficiency
  • ACADSB10q26.132-methylbutyryl-CoA dehydrogenase deficiency
  • ACADVL17p13.1Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency
  • ACAT111q22.3Beta-ketothiolase deficiency (βKT)
  • ACSF316q24.3Combined malonic andmethylmalonic aciduria (CMAMMA)
  • ADA20q13.12Severe combined immunodeficiency (SCID)
  • AHCY20q11.22Hypermethioninemia (MET)
  • ARG16q23Arginase deficiency (ARG)
  • ASL7q11.21Argininosuccinic aciduria (ASA)
  • ASPA17p13.2Canavan disease
  • ASS19q34.1Citrullinemia (CIT) Type I
  • AUH9q22.313-methylglutaconic aciduria (3MGA) Type I
  • BCKDHA19q13.1-q13.2Maple Syrup Urine Disease (MSUD)
  • BCKDHB6q14.1Maple Syrup Urine Disease (MSUD)
  • BLM15q26.1Bloom syndrome
  • BTD3p25Biotinidase deficiency (BIOT)
  • CBS21q22.3Homocystinuria (HCY)
  • CD32019p13.2Methylmalonic acidemia due to transcobalamin receptor defect
  • CFTR7q31.2Cystic fibrosis (CF)
  • CPT1A11q13.2Carnitine palmitoyltransferase I deficiency (CPT IA)
  • CPT21p32Carnitine palmitoyltransferase II deficiency (CPT II)
  • CYP21A26p21.321-hydroxylase deficiency (CAH)
  • DBT1p31Maple Syrup Urine Disease (MSUD)
  • DLD7q31-q32Maple Syrup Urine Disease (MSUD)
  • DNAJC193q26.333-methylglutaconic aciduria (3MGA) Type V
  • DUOX215q15.3Congenital hypothyroidism (CH)
  • ETFA15q23-q25Glutaric acidemia type II (GA2)
  • ETFB19q13.3Glutaric acidemia type II (GA2)
  • ETFDH4q32-q35Glutaric acidemia type II (GA2)
  • FAH15q25.1Tyrosinemia (TYR I, II, III)
  • FANCC9q22.32Fanconi Anemia Type C
  • FMR1Xq27.3Fragile X Syndrome (FXS)
  • G6PC17q21.31Glycogen storage disease type I
  • G6PDXq28Glucose-6-phosphate dehydrogenase deficiency
  • GAA17q25.2-25.3Pompe disease (GAA deficiency)
  • GALC14q31Krabbe Disease
  • GALE1p36-p35Galactosemia Type III
  • GALK117q24Galactosemia Type II
  • GALT9p13Galactosemia Type I
  • GBA1q21Gaucher disease
  • GCDH19p13.2Glutaric acidemia Type I (GA1)
  • GCH114q22.1-q22.2Disorders of biopterin regeneration
  • GJB213q11-q12 Nonsyndromic deafness
  • GJB31p34Nonsyndromic deafness
  • GJB613q12Nonsyndromic deafness
  • GLAXq22Fabry disease
  • GNMT6p12Hypermethioninemia (MET)
  • HADH4q22-q263-hydroxyacyl-CoA dehydrogenase deficiency (M/SCHAD)
  • HADHA2p23Trifunctional protein deficiency (TFP)
  • HADHB2p23Trifunctional protein deficiency (TFP)
  • HBA116p13.3Alpha thalassemia (Hemoglobin Disorder-Var-Hb)
  • HBA216p13.3Alpha thalassemia (Hemoglobin Disorder-Var-Hb)
  • HBB11p15.5 (I ) Sickle cell disease

    (II) Metheglobinemia, beta-globin type

    (III) Beta thalassemia:
    thalassemia major and thalassemia intermedia
  • HCFC1Xq28Methylmalonic acidemia with homocystinuria
  • HEXA15q23Tay-Sachs disease
  • HLCS21q22.13Multiple Carboxylase Deficiency (MCD)
  • HMGCL1p36.1-p353-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMG)
  • HPD12q24.31Tyrosinemia (TYR I, II, III)
  • HSD17B10Xp11.23-hydroxy-2-methylbutyryl-CoA dehydrogenase deficiency (2M3HBA)
  • IDUA4p16.3Mucopolysaccharidosis type I
  • IKBKAP9q31.3Familial dysautonomia
  • IL2RGXq13.1X-linked severe combined immunodeficiency (SCID)
  • IVD15q14-q15Isovaleric acidemia (IVA)
  • LMBRD16q13Methylmalonic acidemia with homocystinuria, cblF type
  • MAT1A10q22Hypermethioninemia (MET)
  • MCCC13q273-methylcrotonyl-CoA carboxylase deficiency (3-MCC)
  • MCCC25q12-q133-methylcrotonyl-CoA carboxylase deficiency (3-MCC)
  • MCEE2p13.3Methylmalonic acidemia
  • MCOLN119p13.2Mucolipidosis type IV
  • MLYCD16q24Malonyl-CoA decarboxylase deficiency (MAL)
  • MMAA4q31.21Methylmalonic acidemia (cblA)
  • MMAB12q24Methylmalonic acidemia (cblB)
  • MMACHC1p34.1 (I) Methylmalonic acidemia (cblC)

    (II) Homocystinuria (HCY)
  • MMADHC2q23.2(I) Methylmalonic acidemia (cblD)

    (II) Homocystinuria (HCY)
  • MTHFR1p36.3Homocystinuria (HCY)
  • MTR1q43Homocystinuria (HCY)
  • MTRR5p15.31Homocystinuria (HCY)
  • MUT6p12.3Methylmalonic acidemia
  • NPC118q11.2Niemann-Pick disease (Type C1)
  • NPC214q24.3Niemann-Pick disease (Type C2)
  • OPA319q13.323-methylglutaconic aciduria (3MGA) Type I
  • OTCXp21.1Ornithine Transcarbamylase Deficiency (OTC)
  • PAH12q22-q24.2Phenylketonuria (PKU)
  • PAX82q13Congenital hypothyroidism (CH)
  • PCBD110q22Disorders of biopterin regeneration
  • PCCA13q32Propionic acidemia (PROP)
  • PCCB3q21-q22Propionic acidemia (PROP)
  • PTS11q22.3Disorders of biopterin regeneration
  • QDPR4p15.31Disorders of biopterin regeneration
  • SLC22A55q23.3Primary carnitine deficiency (CUD)
  • SLC25A137q21.3Citrullinemia Type II (CIT II)
  • SLC25A203p21.31Carnitine-acylcarnitine translocase (CACT)
  • SLC26A47q22.3Pendred syndrome
  • SLC5A519p13.11Congenital hypothyroidism (CH)
  • SMN15q13.2Spinal Muscular Atrophy (SMA)
  • SMPD111p15.4Niemann-Pick disease type A & B
  • TAT16q22.1Tyrosinemia (TYR I, II, III)
  • TAZXq283-methylglutaconic aciduria (3MGA) Type I
  • TCN222q12.2Transcobalamin deficiency
  • TG8q24Congenital hypothyroidism (CH)
  • THRA17q21.1Congenital hypothyroidism (CH)
  • THRB3p24.2Congenital hypothyroidism (CH)
  • TPO2p25Congenital hypothyroidism (CH)
  • TSHB1p13Congenital hypothyroidism (CH)
  • TSHR14q31Congenital hypothyroidism (CH)
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