What is KaryoSeq?

KaryoSeq is a genetic test that utilizes low pass Whole Genome Sequencing for detection of Aneuploidies of all chromosomes and Copy Number Variations (deletions and duplications) >1 Megabase.

Karyoseq Test
Karyoseq Test

Prevalence

Karyoseq Prevalence Karyoseq Prevalence
A woman’s risk of having a pregnancy with certain
chromosomal abnormalities increase with age.
*Source – Combined prevalence using higher end of published ranges from Gross et al. Prenatal Diagnosis 2011; 39, 259-266;

The Risk of having a Baby with Down Syndrome1

26 years old woman
Risk: 1 in 1300
36 years old woman
Risk: 1 in 270
The risk factor increase by almost
5x
However, the incidence of microdeletions is independent of maternal age. In younger women,
the risk for a clinically significant microdeletions exceeds the risk for Down Syndrone.

Why do you need this test?

This is a cost-effective test for identifying aneuploidies of any chromosome as well as copy number variations above 1 Mb.

Applicable for Conditions like:

Any situation that calls for confirmation of a suspected aneuploidy such as trisomy 21, trisomy 18, trisomy 13, Monosomy X or other situations where a possible deletion or duplication is suspected, both in prenatal and postnatal cases.

Karyoseq Advantages

When do you need to get tested?

Prenatal

High risk on maternal serum screening, abnormal ultrasound, family history of chromosomal abnormality, any structural abnormality, miscarriage (products of conception)

Post Natal

Patients with multiple congenital anomalies, autism/autism spectrum disorders (ASDs), and suspected chromosomal imbalances, including micro-deletion syndromes, require specialized care.

Validation

The validation process involved comparison of the CMA results with KaryoSeq.

Sample Size

  • 10 normal
  • 138 abnormal

DNA Sample Type

  • Amniotic Fluid
  • Chorionic villus biopsy
  • Product of conception
  • Direct fetal DNA
  • Peripheral blood DNA

Aberrations Identified

  • Whole chromosome aneuploidies
  • CNVs

Concordance

  • 100% concordance>1Mb CNVs

Here are some CNVs that have been identified

Sl.
No.
Sample TypeMicroarray detected CNV’sSize (Mb)KaryoSeq Detected CNV’sSize (Mb)Concordance (Microarray vs KaryoSeq)
1CVSarr[GRCh38] (18)x3 [Edwards syndrome]80.1Seq[GRCh37]18p11.32 - q23(0_8,077,248)x378
2CVSarr[GRCh38] (21)x3 [Down syndrome]33.1Seq[GRCh37]21p13-q22.3(0-48,129,895)x378
3POCarr[GRCh38] (12)x3133.5Seq[GRCh37]12p13.33 - q24.33(0-133,851,895)x3133.8
4Peripheral Bloodarr[GRCh38]11p15.5q23.3(230,616_116,744,147)x3,
arr[GRCh38]22q11.1q11.21(16,408,174_20,291,006)x1 [DiGeorge syndrome]
116.5
3.88
Seq[GRCh37]11p15.5-q23.3(230,616_116,744,147)x3
Seq[GRCh37]22q11.1-q11.21(16,408,174_20,291,006)x1
103
4
5AFarr[GRCh38] 15q13.2q13.3(30,820,717_32,622,039)x11.8Seq[GRCh37]15q13.2-q13.3(30,885,000_32,485,000)x11.02
6Peripheral Bloodarr[GRCh38] 5q35.2q35.3(175,989,093_178,055,505)x12.0Seq[GRCh37]5q35.2 - q35.3(75,568,094_177,768,094)x12.2
7Peripheral Bloodarr[GRCh38] 22q13.32q13.33(48,199,706_50,759,338)x1 [Phelan-McDermid syndrome]2.5Seq[GRCh37]22q13.32 - q13.33(48,470,380_51,304,566)x12.8
8Peripheral Bloodarr[GRCh38] 22q11.21(18,950,000_21,108,369)x1 [DiGeorge syndrome]2.1Seq[GRCh37]22q11.21(18,762,659_21,870,380)x13
9POCarr[GRCh38]Yq11.23(25,519,063_26,318,566)x2
Yq11.223q11.23(23,717,662_24,887,532)x2
1.1
0.8
Seq[GRCh37]Yq11.223 - q11.23(124,655,552_28,476,607)x23.8
10AFarr[GRCh38] 9q22.1q22.31(87,988,200_92,870,072)x14.8Seq[GRCh37]9q22.1-q22.31(90,521,336_95,971,336)x15.4
11POCarr[GRCh38] 10q22.3(79,625,681_80,213,053)x1,
arr[GRCh38]15q11.2q13.1(23,102,621_28,458,904)x1 [Angelman syndrome/ Prader-Willi syndrome]
0.6
5.3
Seq[GRCh37]10q11.22(18,762,659_21,870,380)x1
Seq[GRCh37]15q11.2 - q13.1(18,762,659_21,870,380)x1
3.3
5.1
12Peripheral Bloodarr[GRCh38] 18q21.2q21.33(54,720,552_62,003,701)x17.2Seq[GRCh37]18q21.2 - q21.33(52,309,136_59,709,136)x17.4
13Peripheral Bloodarr[GRCh38] 13q32.3q34(101,067,948_114,342,258)x1,
arr[GRCh38]16p13.3p13.2(35,881_8,831,829)x3
13.2
8.7
Seq[GRCh37]13q33.1-q34(101,770,197_115,169,878)x1
Seq[GRCh37]16p13.3-p13.2(5,260,000_8,910,000)x3
13.3
3.6
14AFarr[GRCh37] 10p15.3p14(100,048_7,701,527)x17.6Seq[GRCh37]10p15.3-p14(0_7,660,000)x110
15Peripheral Bloodarr[GRCh38] 2q12.3q13(108,652,368_110,116,258)x11.2Seq[GRCh37]2q12.3 - q13(109,200,000_111,051,337)x11.4
16Peripheral Bloodarr[GRCh38] 21q11.2q21.3(13,644,166_25,925,065)x112.2Seq[GRCh37]21q11.2 - q21.3(15,500,000_26,800,422)x111.3
17Peripheral Bloodarr[GRCh38] 8q24.21q24.3(130,350,392_145,070,385)x314.7Seq[GRCh37]8q24.21-q24.3(131,400,277_144,250,277)x312.9
18Peripheral Bloodarr[GRCh38]5p15.33p15.2(113,462_13,788,173)x1 [Cri du chat syndrome]
arr[GRCh38]20p13p12.1(80,929_15,514,914)x3
13.7
15.5
Seq[GRCh37]5p15.33 - p15.2(0_13,810,000)x1
Seq[GRCh37]20p13 - p12.1(0_13,810,000)x3
13.8
15.6
19Peripheral Bloodarr[GRCh38] 16p11.2(29,568,701_30,166,595)x10.5Seq[GRCh37]16p11.2 - q11.2(31,910,000_46,800,515)x114.8
20Peripheral Bloodarr[GRCh38] 7p21.3p15.2(10571965-26444007)x115.8Seq[GRCh37]7p21.3 - p15.2(10,560,000_26,460,000)x115.9
21Peripheral Bloodarr[GRCh38] 13q22.2q31.3(75,664,252_91,427,209)x115.7Seq[GRCh37]13q22.2 - q31.3(76,120,197_92,110,324)x116
22Peripheral Bloodarr[GRCh38] 9q34.3(137,434,967_138,124,196)x10.7Seq[GRCh37]9p13.1 - q12(38,814,048_55,146,786)x116.33
23Peripheral Bloodarr[GRCh38] 4q34.1q35.2(172,079,686_190,036,305)x117.9Seq[GRCh37]4q34.1 - q35.2(172,981,307_191,154,276)x118.2
24POCarr[GRCh38] (13)x3 [Patau syndrome]95.6Seq[GRCh37]13p13.1 - q12(0_115,169,878)x323
25AFarr[GRCh38]6q26q27(162,350,656_170,610,394)x1,
arr[GRCh38]7q33q36.3(133,640,234_159,327,017)x3
8.3
25.7
Seq[GRCh37]6q26-q27(162,025,576_171,115,067)x1
Seq[GRCh37]7q33-q36.3(133,113,445_159,138,663)x3
9
26
26POCarr[GRCh37] (19)x158.6Seq[GRCh37]19q13.2(8,404,119_49,024,030)x140.6
27CVSarr[GRCh38] (20)x3
arr[GRCh38](21)x3 [Down syndrome]
64.2
33.1
Seq[GRCh37]20p13 - q13.33(0-63,025,520)x3
Seq[GRCh37]21p13 - q21.2(0_25,800,422)x3;
Seq[GRCh37]21q21.2 - q22.3(25,800,422_48,129,895)x3
63
25.8
22.3
28POCarr[GRCh38] Xp22.33q28(251,880-156,004,066)x1 [Turner syndrome]155.7Seq[GRCh37]Xp22.33 - q28(0_149,158,438)x1
Seq[GRCh37]Xq28(:149,158,438_153,908,438)x1
Seq[GRCh37]Xq28(153,908,438_155,270,560)x1
149
4.7
1.3
29POCarr[GRCh38] Xp22.33q28(2,785,592_155,691,858)x2[Klinefelter syndrome]155.7Seq[GRCh37]Xp22.33 - q28(0_155,270,560)x3155.2
30CVSarr[GRCh38]Xp22.33q28(2,785,592_155,691,858)x2[Klinefelter syndrome]155.7Seq[GRCh37]Xp22.33 - q28(0_155,270,560)x3155.2
CVS: Chorionic Villus Sampling; POC: Products of conception; AF: Amniotic Fluid;

Why MedGenome?

  • Well Validated test
  • Largest CAP-accredited and NABL-certified Genomics sequencing lab in South Asia

Technical Details

It is a low pass Whole Genome Sequencing test and data is analyzed using bioinformatics algorithms.

Test CodeTest NameSample RequirementsTATMethodology
MGM2754Karyoseq (without MCC or other samples)Peripheral Blood, Direct DNA8 Working DaysNGS
MGM2777KaryoSeq with MCCChorionic Villus Sampling (CVS)/Amniotic Fluid (AF)/Cultured Amniotic Fluid/Cord Blood/Cardiac Blood/Products of Conception Tissue (POC)/Peripheral Blood, Direct DNA/DNA Isolated from Cell Lines or Cultured Cells10 Working DaysNGS
MGM2761Karyoseq with (prenatal cell culture if required)Chorionic Villus Biopsy, Amniotic Fluid8 + 12 Working DaysNGS

Sample Details

Chorionic Villus Sampling (CVS)
Chorionic Villus Sampling (CVS)
Amniotic Fluid (AF)
Amniotic Fluid (AF)
Cultured Amniotic Fluid
Cultured Amniotic Fluid
Cord Blood
Cord Blood
Cardiac Blood
Cardiac Blood
Products of Conception Tissue (POC)
Products of Conception Tissue (POC)
Peripheral Blood, Direct DNA
Peripheral Blood, Direct DNA
DNA Isolated from Cell Lines
DNA Isolated from Cell Lines

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