SNP-Chip Microarray

6.0 DNA-SNP Microarray probes cover the entire human genome and are designed to detect:  
  1. All microdeletions/microduplications throughout the genome including many known syndromes.
  2. All numerical chromosome abnormalities including trisomies, monosomies, unbalanced translocations, mosaicism and supernumerary (marker) chromosomes.

BENEFITS: This new advance is valuable and important and WILL:

  1. Enable recognition of significant and often unexpected microdeletions/duplications throughout the genome (Y-chromosome excluded). The coverage is MORE EXTENSIVE AND LESS EXPENSIVE THAN ANY OTHER EQUALLY COMPREHENSIVE AVAILABLE MICROARRAY.
  2. Recognize microdeletions/duplications not determinable by gene sequencing and be valuable in detecting these abnormalities in about 10% of those with autism.
  3. Add a 10-20% detection rate to the diagnosis of unexplained intellectual disability/congenital malformations after negative results on karyotyping.
  4. Not only target specific disorders, as in other microarrays, but cover the genome including subtelomeric regions, supplemented by an additional assay at no extra cost.
  5. Be valuable in those individuals with intellectual disability and/or anomalies who have previously been determined to have “balanced chromosome rearrangements.”
  6. No longer require separate assays for routine comparative genomic hybridization or subtelomeric chromosome analysis.
  7. Recognize uniparental disomy for any autosomal chromosome pair (when specifically ordered).


  1. Samples are analyzed at a resolution of 50 Kb for known microdeletion/duplication syndromes and subtelomeric regions. The remaining genome is analyzed at a resolution of 200 Kb (deletions less than 200 Kb and duplications less than 500 Kb are not reported).
  2. Balanced structural rearrangements (balanced translocations, inversions) will not be detectable.
  3. Single gene mutations usually determinable by gene sequencing will not be detectable.


A. HIGH DETECTION RATES [percent detection ranges from 50 to over 99%]
Angelman syndrome 15q11.2-q12 deletion
Cat eye syndrome inv dup(22)(q11.2)
Congenital adrenal hypoplasia Xp21.2 deletion
Cri-du-Chat syndrome 5p15.2-p13.3 deletion
Deletion/Duplication Syndromes
deletion and/or duplication/triplication 1p36
deletion syndrome 3q29
deletion syndrome 9q34.3
deletion syndrome 15q21
Inversion duplication/deletion 8p23.1 8p
duplication syndrome 22q11.2
15q11.2-q12 (PWS AS) duplication 15q11.2-q12
DiGeorge, Velocardiofacial syndrome 22q11.2 deletion
DiGeorge syndrome 2 10p14 deletion
Dosage sensitive sex reversal Xp21.2 duplication
Jacobsen (11q25 deletion) syndrome 11q24-q25
Langer-Giedion syndrome 8q23.3-q24.11 deletion
Leri-Weill dyschondrosteosis Xp22.33/Yp11.32
Miller-Dieker lissencephaly syndrome 17p13.3 deletion
Nephronophthisis 1 2q13 homozygous deletion
Pelizaeus-Merzbacher disease Xq22 duplication or deletion
Prader-Willi syndrome 15q11.2-q12 deletion
Prader-Willi/Angelman duplication 15q11.2-q12
Potocki-Shaffer syndrome 11p11.2 deletion
Smith-Magenis syndrome 17p11.2 deletion
Smith-Magenis syndrome duplication 17p11.2
Steroid Sulfatase Deficiency Xp22.31 deletion/duplication
Williams-Beuren syndrome 7q11.23 deletion/duplication
Wolf-Hirschhorn syndrome 4p16.3 deletion
B. DISORDERS WITH INTERMEDIATE DETECTION RATES [percent detection ranges from 5 to 35%]
Autism spectrum Multiple sites
Alagille syndrome 20p12.2 deletion
Aniridia 11p13 deletion
Deletion Syndrome 2q22.3
Glycerol kinase deficiency Xp22 deletion
Greig cephalo-polysyndactyly syndrome 7p14.1 deletion
Neurofibromatosis II 22q12.2 deletion
Retinoblastoma 13q14.2 deletion
Rett syndrome Xq28 deletion/duplication
Rubinstein-Taybi syndrome 16p13.3 deletion
Saethre-Chotzen syndrome 7p21.1 deletion
Sex reversal X/Y translocations Yp11.31 deletion
Trichorhinophalangeal syndrome 1 8q23.3 deletion
Tuberous sclerosis 1 9q34.2 deletion
WAGR syndrome 11p13 deletion
Wilms tumor 11p13 deletion
C. DISORDERS WITH LOW DETECTION RATES [percent detection uncertain or less than 5%]
Autism spectrum 15q11.2-q13, 16p11.2, 22q13.3
Autism spectrum Xp22.32 deletion
Basal cell nevus syndrome 9q22.32 deletion
Beckwith-Wiedemann syndrome 11p15.5 deletion/duplication
Bruton agammaglobulinemia Xq22.1 deletion
Campomelic dysplasia 17q24.3 deletion
CHARGE syndrome 8q12.2 deletion
Cleidocranial dysplasia 6p21.1 deletion
Congenital diaphragmatic hernia 15q26.1-q26.2 deletion
Cornelia de Lange syndrome 5p13.2 deletion
Dandy-Walker syndrome 3q24 deletion
Down syndrome critical region 21q22 duplication
Feingold syndrome 2p24.3 deletion
Holoprosencephaly 1 21q22.3 deletion
Holoprosencephaly 2 2p21 deletion
Holoprosencephaly 3 7q36.3 deletion
Holoprosencephaly 4 18p11.31 deletion
Holoprosencephaly 5 13q32.3 deletion
Holoprosencephaly 7 Missense mutations
Hypoparathyroidism, sensorineural deafness and renal disease 10p14 duplication
Kallmann syndrome 1 Xp22.31 deletion
Leukodystrophy 11q14.2-q14.3 deletion
Mental retardation X-linked with growth hormone deficiency Xq27.1 deletion or duplication
Microphthalmia with linear skin defects Xp22.2 deletion
Nail-patella syndrome 9q33.3 deletion
Neurofibromatosis I 17q11.2 deletion
Noonan syndrome 12q24.13 deletion
Rieger syndrome, type 1 4q25 deletion
Split-Hand/foot malformation-3 10p14 duplication
Sotos syndrome 5q35 deletion
X-linked heterotaxy Xq26.3 deletion
*Note that microdeletion/duplication analysis establishes a diagnosis in the vast majority of disorders listed in Section A. The occurrence of microdeletions/duplications in disorders listed in Sections B and C is much less frequent or very infrequent. Gene sequencing is available for an increasing number of these disorders including Tuberous Sclerosis type 1, Noonan syndrome, CHARGE syndrome, Rett syndrome and Neurofibromatosis types 1 and 2.