Karyotyping is a test to examine chromosomes in a sample of cells, which can help identify genetic problems as the cause of a disorder or disease (here is a reference from MedlinePlus). Traditional karyotyping is done by Giemsa staining of chromosomes. The ideogram of a human sample looks like this:

 a Quantum Leap in Quality, a Fraction of the Cost, a Revolution of Karyotyping

InKaryo's eKaryotype 3000 technology takes a small amount of human sample of saliva, cheek swab, blood, tumor, a biopsy, or FFPE, extracts genomic DNA, executes whole genome sequencing, performs bioinformatics analysis, and generates a diagnostic report to detect a gain or loss of chromosomal DNA (chromosomal aneuploidy) that associates with developmental delay, mental retardation, multiple congenital anomaly, autism spectrum disorder, mental disorder, depression, and infertility. InKaryo's massive parallel shotgun sequencing (MPSS) protocol and proprietary bioinformatics analysis reinvented karyotyping with a leap in quality yet at a fraction of the cost comparing to florescence in situ hybridization (FISH), array based comparative genomic hybridization (aCGH), or chromosomal microarray analysis (CMA). Through massive parallel shotgun sequencing (MPSS), our technology will cover the whole genomic regions evenly with highly specific and accurate digital sequence output, whereas all hybridization based technologies (microarray or FISH) typically covers certain targeted chromosomal regions with analog signal output. Our bioinformatics analysis will further correct all major technical and biological biases, and generates a highly accurate report. 

The graphs below show a comparison of InKaryo's eKaryotype 3000 versus a SNP based array CGH analysis (please click each graph to see enlarged details).

Competitor's CGH array karyotype Click the graph to see the zoom-in details. The is a male sample karyotyping results across all 24 chromosomes. The middle grey area is centered around copy number 2. The red line area below the grey area indicates copy number less than 2 (deletion event for autosomes and female X chromosomes). The green line area above the grey area indicates copy number greater than 2 (amplification event). Please note that the noise level from CGH array is high.

InKaryo's eKaryotype Click the graph to see the zoom-in details. The is a male sample eKaryotyping results across all 24 chromosomes. The middle grey area is centered around a thin line which is quantitatively of copy number 2. The thick red lines below the grey area are quantitatively of copy number 1 or 0 (deletion event for autosomes and female X chromosomes). The thick green lines above the grey area are quantitatively of copy number 3 or 4 (amplification event). eKaryotype 3000 results are not only of low noise, but highly quantitative.

 

The graphs below show a comparison of InKaryo's eKaryotype 3000 versus an oligo CGH array analysis. 

 

The x-axis represents the probes position across the full X chromomosme. A female sample (Blue) with 2 copies of X chromosome is expected to have a log2 ratio of 0.0 A male sample (Red) with 1 copy of X chromosome is expected to have a log2 ratio of -1.0 This CGH assary results barely distinguish between 1 and 2 copies of full chromosome.

The x-axis represents the 1 MB bin position across the full X chromomosme. A female sample (Blue) with 2 copies of X chromosome are expected to have a log2 ratio of 0.0 A male sample (Red) with 1 copy of X chromosome are expected to have a log2 ratio of -1.0 Our eKaryotype results clearly distinguish between 1 and 2 copies of chromosome at 1 MB resolution.

Disclaim: The ekaryotype 3000 is for research use only.