Novemb er 2018

SNP Array Identifies Inherited Genetic Disorder
Contributing to IVF Failures
Human Karyomap-12 Array identifies balanced translocation carriers and translocation
abnormalities in blastocysts for informed IVF embryo selection.
Introduction
In January 2016, Shanghai Ji Ai Genetics and IVF (GIVF) Institutebecame the first institute in China to see the birth of a baby
conceived using karyomapping and in vitro fertilization (IVF).
Karyomapping is an advanced preimplantation genetic diagnosis(PGD) technique that assesses an embryo for a specific singlegene condition before transfer into the uterus. The goal is tominimize the risk of couples carrying a known inherited genetic
disorder of having children affected with that disorder.
Of the known inherited genetic disorders, balanced translocations,
including reciprocal and Robertsonian translocations, impact 0.19% of
the general population, but its prevalence increases to 2.2% in IVF
patients who have a history of recurrent miscarriages or repeat IVF
failures.1 Balanced translocations vary from single-gene disorders.
Carriers possess a balanced form of the rearrangement and suffer fromno health issues.
Current PGD technologies, such as modified fluorescent in situ
hybridization (FISH) and next-generation sequencing (NGS)
approaches, are time consuming and can’t distinguish between
embryos with balanced and structurally normal chromosomes, andreciprocal and Robertsonian translocation carrier.2-4
In 2017, researchers at Shanghai Ji Ai decided to test the ability ofkaryomapping to detect the presence of balanced translocations. They
performed a blinded clinical study of 11 translocation families
undergoing IVF using the Human Karyomap-12 Array.5 All families hada history of recurrent spontaneous abortion, infertility, or pregnancies
with chromosome abnormalities

assure IVF parents that their children will be born without known
congenital anomalies.
Q: How did your lab identify balanced translocation cases initiallyand what were the difficulties?
Zhang Shuo (ZS): Prior to the development of our PGH method,
we used FISH to analyze embryos from balanced translocation
patients, which was time consuming. Faster technologies, suchas SNP arrays, analyze only chromosome copy number variations(CNV) and therefore cannot be used to detect chromosome
structure abnormalities in diploid embryos.
As a result, diagnosis of transplanted embryos for balanced
translocations is difficult. That’s a problem for IVF patients who arecarriers. There is the potential that their child will possess anunbalanced translocation and will be born with congenital defects.
There is also a 50% probability their embryos could be carriers of
the same chromosome translocation that they possess, increasing
the risk of transferring a detrimental allele to subsequent
generations.
Q: How did you develop your new PGH method?
ZS: We theorized that whole-genome karyomapping had thepotential to diagnose embryos with chromosomal structureabnormalities, such as reciprocal and Robertsonian translocations.
Karyomapping uses linkage-based genome-wide haplotyping toprovide a high-density view of chromosomes and insight into
inherited alleles.

iCommunity spoke with several members of the Shanghai Ji Ai team,including Professor Sun Xiao-xi, President of Shanghai Ji Ai; Professor
Zhang Yueping, Director, Genetics Department; and Zhang Shuo,Senior Technician of Preimplantation Genetic Diagnosis, about thisstudy and the value of preimplantation genetic haplotyping (PGH) in
identifying translocations and limiting their transmission to offspring.
Q: What is the incidence of congenital birth defects and genetic
disease in China?
Sun Xiao-xi (SX): Our country has a high incidence of congenital
disorders. An estimated > 1 million children are born each yearwith birth defects in China, approximately 5.6% of the total
number of births.6 It has seriously affected the quality of life andhealth of our children and impacted their families and the generalcommunity. The leading causes of birth defects are complex andchromosomal diseases. Through karyomapping, we hope toFor Research Use Only. Not for use in diagnostic procedures.

Professor Sun Xiao-xi, President; Professor Zhang Yueping, Director, Genetics
Department; and Zhang Shuo, Senior Technician of Preimplantation Genetic
Diagnosis at Shanghai Ji Ai Genetics and IVF Institute in Shanghai, China.

1570-2018-008 | 1

Novemb er 2018

First, we chose the genetic marker type to use in performing astudy. Short tandem repeat (STR) loci analysis is a difficult andtime-consuming analysis to perform, especially on multiple DNA
sources (family members and embryos). We chose SNPs as ourgenetic marker, which offer a faster, streamlined workflow. WithSNPs, we can perform linkage analysis between parents,
reference samples, and embryos easily. We researched thevarious SNP-arrays on the market and chose the 300,000 SNP
HumanKaryomap-12 Array on the iScan™ System. It enables
simultaneous analysis of molecular haplotypes and aneuploidy
screening for each embryo and includes easy-to-use BlueFuse™
Multi Software for data analysis.

Q: What were the results of the study testing the ability of thisPGH method to identify balanced and structurally normal
embryos?
ZS: Eleven translocation families were enrolled in the study. In
addition to the prospective parents and certain close relatives, 68
blastocysts were analyzed in which 42 were unbalanced and 26
were balanced. We identified 13 embryos with structurally normal
chromosomes and these were transferred back into thecorresponding IVF patients. Prenatal cytogenetic analysis ofamniotic fluid cells was performed after the second trimester. The
results predicted by PGH were consistent with the cytogeneticanalysis.

"The HumanKaryomap-12 Arrayenables simultaneous analysis ofmolecular haplotypes and aneuploidy
screening.""Our method can identify haplotypes inchromosomes or breakpoint regions
genome wide to identify the presenceof any type of translocation."

Q: How did you decide which SNPs to use in detecting balanced
and structurally normal translocations?
ZS: We identified informative SNPs that were used to establish thehaplotypes (DNA variations inherited together). For our study, thehaplotypes consisted of the breakpoint regions, the wholechromosomes involved in the translocations, and thecorresponding normal homologous chromosomes in the couple,reference (a family member or an unbalanced embryo), and theembryos.

Q: What are the advantages of this new PGH method?
ZS: Our PGH genome-wide haplotype linkage analysis method
has several advantages. It identifies the haplotypes in thebreakpoint regions. It detects homologous recombination in thebreakpoint regions by simultaneously identifying the haplotypes of
the two whole chromosomes involved in the translocation and thetwo corresponding normal homologous chromosomes. It provides
information to improve the clinical pregnancy rate by determining
which embryos are translocation carriers and screening all
chromosomes for aneuploidy, simultaneously. Finally, our method
can identify haplotypes in chromosomes or breakpoint regions
genome wide to identify the presence of any type of translocation.

The selection criteria were that the SNPs should be heterozygous
in the carrier, homozygous in his/her partner, and homozygous in
the carrier’s parents or other family members. This information wasused to determine which of the carrier’s two haplotypes werelinked to the derivative chromosome or the normal chromosome.
The predictive criterion to distinguish embryos with balanced andstructurally normal chromosomes combined the haplotypes ofbreakpoint regions and the presence of homologous
recombination in those regions.
Q: Describe the PGH process used to perform balanced
translocation analysis?
Zhang Yueping (ZY): The process involves genome-wide SNP
genotyping with the Human Karyomap-12 Array of DNA samples
from the IVF couple, their parents, and embryos. We use BlueFuse
Multi Software to perform linkage analysis and model the patientfamily genome-wide haplotype. If the carrier’s balanced
translocations were inherited, building the family haplotype
requires analyzing the DNA of a close family relative to use as areference. If it’s a de novo family mutation, we use an embryo withan unbalanced translocation as the reference.

For Research Use Only. Not for use in diagnostic procedures.

Most importantly, our PGH method is relatively simple andefficient, and suitable for routine clinical application. The entire
process can be completed within 48 hours, with data analysis
taking less than two hours of the total time.

"Most importantly, our PGH method isrelatively simple and efficient, andsuitable for routine clinical application."
Q: Do you now perform karyomapping for every embryo sample?
ZY: For the past few years, we used the HumanKaryomap-12
Array to identify only single-gene defects of embryo biopsies. We
now use it on all potential IVF embryos to identify single-gene
defects and structural chromosomal abnormalities, such astranslocations.
Q: What is the significance of this breakthrough in the detection ofbalanced translocation IVF patients for clinical diagnosis?
SX: China has millions of seemingly healthy chromosome
balanced translocation patients with the potential of passing along
the chromosome abnormality to subsequent generations.
Development of this genome-wide haplotype linkage analysis

1570-2018-008 | 2

Novemb er 2018technology is an important breakthrough in the field of humanassisted reproductive medicine in our country and demonstrates
our leadership in the field. It improves the success of IVF
treatments, particularly in patients who have suffered fromrecurrent miscarriages. For balanced translocation patients, thetechnology ensures that they won’t pass the translocation
chromosomes they possess along to their offspring.

Learn more about the products and systems
mentioned in this article:
HumanKaryoMap-12 Array, www.illumina.com/products/bytype/clinical-research-products/human-karyomap.html
iScan System, www.illumina.com/systems/arrayscanners/iscan.html
BlueFuse-Multi Software, www.illumina.com/clinical/clinical_
informatics/bluefuse.html

References1.

Zhang S, Lei C, Wu J, et al. The establishment and application ofpreimplantation genetic haplotyping in embryo diagnosis for reciprocal andRobertsonian translocation carriers BMC Med Genomics. 2017; 10(1):60.
doi: 10.1186/s12920-017-0294-x.

2.

Weier HU, Munn S, Fung J. Patient-specific probes for preimplantation
genetic diagnosis of structural and numerical aberrations in interphase cells.

J Assist Reprod Genet. 1999; 16:182−191.
3.

Lersch RA, Fung J, Munné S, et al. Case-Specific, Breakpoint-Spanning
DNA Probes for Analysis of Single Interphase Cells. Genet Test. 2000;
4:273−278.

4.

Hu L, Cheng D, Gong F, et al. Reciprocal Translocation Carrier Diagnosis in
Preimplantation Human Embryos. EBioMedicine. 2016; 14:139−147.

5.

Alfarawati S, Fragouli E, Colls P, et al. First births after preimplantation
genetic diagnosis of structural chromosome abnormalities using comparative
genomic hybridization and microarray analysis. Hum Reprod. 2011;26:1560−1574.

6.

Zhao W, Wu M, Chen F, et al. Robertsonian Translocations: An Overview of872 Robertsonian Translocations Identified in a Diagnostic Laboratory inChina. PLoS One. 2015; 10(5): e0122647.

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see www.illumina.com/company/legal.html. Pub. No. 1570-2018-008 QB 6160

For Research Use Only. Not for use in diagnostic procedures.

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