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xGen® Inherited Diseases Panel

The xGen® Inherited Diseases Panel consists of 116,355 individually synthesized and quality controlled xGen Lockdown® Probes designed for targeted enrichment of 4503 genes and 180 SNPs associated with inherited diseases. The panel enables deeper sequencing of these genes, increasing the ability to detect disease-causing mutations. The gene list is based on the HGMD® (Human Gene Mutation Database) repository of known inherited disease-causing mutations and was refined by the Emory Genetics Laboratory at Emory University for clinical significance and relevance.

Benefits

  • High uniformity across all targets
  • Easily expanded by adding custom xGen® Lockdown® Probes
  • Can be spiked into Nimblegen or Illumina exome capture kits to enhance their sensitivity
  • Easy online ordering and next-day shipping 

Features

  • 116,355 xGen® Lockdown® Probes targeting 4503 genes and 180 SNPs
  • Individually synthesized and quality controlled probes
  • Targets based on the HGMD® and defined in collaboration with Emory Genetics Laboratory
  • Validated with the xGen 4-hour Capture Protocol developed at IDT


xGen® Inherited Diseases Panel

The xGen® Inherited Diseases Panel comprises 116,355 xGen Lockdown Probes targeting 4503 gene and 180 SNPs associated with inherited diseases. The panel is available in 2 sizes—16 reactions and 96 reactions.

ProductPricing
16 rxn xGen® Inherited Diseases Panel v1.0$2,400.00 USD
96 rxn xGen® Inherited Diseases Panel v1.0$14,400.00 USD

Introduction

Whole exome sequencing has traditionally been the standard method for detecting a wide variety of inherited diseases. In addition to providing poor coverage of many disease-causing mutations, exome capture panels often waste sequencing reads on irrelevant genomic regions. The xGen® Inherited Diseases Panel was developed in collaboration with the Emory Genetics Laboratory (EGL) at Emory University as a single panel that targets all disease-causing mutations as defined by the HGMD® database. The Inherited Diseases Panel combines the ease of whole exome sequencing with the low per sample cost of targeted panels.

Source: http://ww2.aievolution.com/acm1401/index.cfm?do=abs.viewAbs&abs=2070

Panel

The xGen® Inherited Diseases Panel targets exons in 4503 genes, and 183 SNPs. Genes associated with the following disorders are included in this single enrichment panel:

Disease
No. of Genes on Panel
Autism Spectrum Disorders 60
Cardiomyopathy 93
– Arrhythmias 29
– Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy 7
– Brugada Syndrome 8
– Dilated Cardiomyopathy 25
– Hypertropic Cardiomyopathy 14
– Long and Short QT Syndrome 12
– Pulmonary Arterial Hypertension 4
– Sudden Cardiac Arrest 10
– Thoracic Aortic Aneurysm & Dissection and Related Disorders 6
Ciliopathies 112
Congenital Disorders of Glycosylation 66
Congenital Myasthenic Syndromes 11
Epilepsy and Seizure Disorders 108
Eye Disorders 205
– Achromatopsia, Cone, and Cone-Rod Dystrophy 36
– Albinism 5
– Anophthalmia/Microphthalmia/Anterior Segment Dysgenesis/Anomaly 22
– Bardet-Biedl Syndrome 18
– Congenital Stationary Night Blindness 15
– Flecked-Retina Disorders 6
– Joubert Syndrome 18
– Leber Congenital Amaurosis 18
– Macular Dystrophy/Degeneration/Stargardt Disease 16
– Neuronal Ceroid Lipofuscinoses 11
– Optic Atrophy 5
– Retinitis Pigmentosa 65
– Senior Loken Syndrome 7
– Stickler Syndrome 5
– Usher Syndrome 13
– Vitreoretinopathy 9
Comprehensive Glycogen Storage Disorders 20
– Glycogen Storage Disorders: Liver 11
– Glycogen Storage Disorders: Muscle 12
Hearing Loss 87
Hereditary Cancer Syndrome 46
Hereditary Periodic Fever Syndromes 7
Inflammatory Bowel Disease 22
Lysosomal Storage Disorders 55
Maturity Onset Diabetes of the Young 4
Multiple Epiphyseal Dysplasia 7
Neuromuscular Disorders 46
– Congenital Muscular Dystrophy 18
– Limb-Girdle Muscular Dystrophy 26
Noonan Syndrome and Related Disorders 12
Peroxisome Biogenesis Disorders, Zellweger Syndrome Spectrum 15
Short Stature Panel 40
Skeletal Dysplasia 162
X-Linked Intellectual Disability 92

Source: http://genetics.emory.edu/egl/about/index.php/1583

Design Information

Higher Coverage Uniformity, Consistent Performance, High Reproducibility

The data presented in Figures 1–3 demonstrate the excellent performance of the xGen® Inherited Diseases Panel. Target enrichment was performed using the xGen Rapid Capture Protocol v1 (4-hour hybridization) and data were normalized to 25M reads. The average sample insert size was 344 bases with a standard deviation of 35 bases. The range of on-target reads was 14.3–14.9M with 4.6–5% duplicate reads.

High Uniformity of Coverage

Figure 1. Highly Uniform Coverage from xGen® Inherited Diseases Panel. Uniformity of coverage of the target regions is represented here as proportion of targets with >0.2 x mean coverage (blue), >0.5 x mean coverage (green) and >1.0 x mean coverage (grey). The data demonstrate that with a mean coverage depth of 100X, 99% of the targets captured using the xGen® Inherited Diseases Panel will have >20X depth of coverage. Error bars indicate standard deviation from the mean.

Complete Coverage Across All Targets

Figure 2. Complete Coverage of Targeted Regions Using xGen® Inherited Diseases Panel. Uniformity of coverage for 2 replicate captures using the xGen® Inherited Diseases Panel were compared. The 2 experiments had practically identical coverage, with both achieving 98.7% of all targets covered at ≥30X using 25M reads on the Illumina MiSeq® Sequencing System (300-base paired-end reads).

Consistent Performance and High Reproducibility

Figure 3. High Reproducibility Obtained Using xGen® Inherited Diseases Panel. A comparison of target-by-target coverage between 2 sample replicates captured using the xGen® Inherited Diseases Panel shows excellent reproducibility, with an R2 value of 0.9622, demonstrating the consistent, high performance of the panel.