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Human genetics research
Monogenic to multifactorial disease genetics: how do we improve efficiency?
When we study rare and inherited diseases, we find a wide spectrum of genetic and phenotypic heterogeneity and an equally wide selection of causative mutation types. No single platform is capable of finding all causative variants with the speed and cost efficiency needed in a typical research setting.
Here are examples of human genetic disease projects and technology solutions that can deliver meaningful data within a week from sample to data.
Whether you need to analyse one gene or thousands of genes, we enable you to select the right tool for the job, helping you to find answers more efficiently.
Educational content
What technologies should you consider for different problems in human genetics?
Single-gene inheritance pattern (Mendelian disease)
See how you can quickly identify causative alleles in inherited diseases through candidate gene analysis using next generation sequencing of custom-assembled gene panels.
Molecular analysis of inherited cardiomyopathy using next generation semiconductor sequencing technologies - Chaoxia Lu et al
Approach:
- Identify causative variants of different inherited cardiomyopathies using a single Ion AmpliSeq gene panel.
- Perform targeted next-generation sequencing (NGS) on candidate genes.
- Verify genetic variants by Sanger sequencing.
Results:
- Potential pathogenic variants found in 23.6% of study samples, including a homozygous variant in the SLC25A4 gene.
- Of the pathogenic variants found, 15 had been reported in the Human Gene Mutation Database or ClinVar database, while 11 were novel.
- Most variants were found in MYH7 (8/26) and MYBPC3 (6/26) gene. Titin (TTN) truncating mutations account for 13% of the dilated cardiomyopathy cases (3/23).
About the technology
| For multiplex analysis of multiple genes, multiple samples for low cost variant detection: | |||
 |  | ||
 | |||
| For single gene, single sample variant detection or NGS verification: | |||
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Multi-factorial (non-Mendelian) disease
Inherited diseases can also be caused by a combination of genetic loci which together result in potentially complex and variable phenotype, making disease identification more difficult. We show how a combination of chromosomal microarray analysis (CMA) and whole exome analysis (WES) can improve discovery rates over WES alone.
How can we identify non-Mendelian loci and quantify their contribution to disease?
Recent studies have shown that a combination of genomic array and sequential exome analysis, is an effective approach in the evaluation of subjects with unexplained intellectual disability, autism spectrum disorder and/or congenital anomalies. The expected clinical yield of these tests are for high resolution genomic array 15-20% and in combination with exome sequencing >50% (Vissers L et al. Nature Genetics, 2010, PMID: 21076407).
Example: Autism study
Molecular diagnostic yield of chromosomal microarray analysis and whole exome analysis using next-generation sequencing in children with autism spectrum disorder. Tammimies K et al. (2015) JAMA
Approach:
- Collect research samples from 258 unrelated children with Autistic Spectrum Disorder (ASD)
- Perform chromosomal microarray analysis (CMA)
- Perform whole exome sequencing (WES) on 100 probands, where DNA samples from both parents are available
Results:
- Of 258 probands, 24 identified pathogenic alleles from CMA and 8 of 95 from WES
- 96 de novo variants that could be contributive were also identified
About the technology
Non-familial congenital & germline disorders Reproductive health research Complex traits & pharmacogenomics
Trinucleotide repeat disorders
Incurable neurodegenerative diseases such as Huntington’s disease, spinocerebellar ataxias, fragile X syndrome, and SBMA are caused by unstable repetitive triplet elements within defined loci. Variability in repeat length is observed in normal alleles and can range from 15 to 40 nucleotides. Pathology results when repeat length exceeds a specific threshold, usually greater than 45. The disease phenotype may worsen from generation to generation due to de novo germline expansion of repeats.
How can we find disease-causing simple tandem repeat variants?
Example: Fragile X
More than 30 Mendelian disorders are linked to STR expansions. In Fragile X syndrome, tandem CGG repeats within the FMR1 gene are associated with onset and severity of frontotemporal dementia and amyotrophic lateral sclerosis.
Approach:
- The FMR1 CGG repeat region can range in size, and analysis of the gene requires resolution of long fragment lengths of 800bp or more
- Perform fragment sizing (fragment analysis) by capillary electrophoresis sequencing using the Applied Biosystems SeqStudio Genetic Analyzer and Asuragen AmplideX PCR/CE FMR1 and C9orf72 reagents
- Amplify the Asuragen AmplideX PCR/CE FMR1 and C9orf72 reagents from blood samples taken from Fragile X research subjects
- Run the AmplideX PCR/CE FMR1 and C9orf72 reagents under the following run parameters: SeqStudio module = LongFragAnalysis (modified), injection time = 2 sec, injection voltage = 6 kV, run time = 3,300 sec, and run voltage = 6 kV
- Run time takes around 30 minutes
Results:
- Consistent detection of expected n and n + 1 alleles demonstrates single-repeat assay resolution.
- Genotype and allele repeat lengths were 100% concordant with expected values.
About the technology
How do new mutations arise in families that don’t have a history of the disease?
How to find these causative mutations?
Example: Primary Ciliary Dyskinesia Case Study
A rare genetic disorder of ciliary function, affecting 1/20,000 live births, this disease has phenotypic heterogeneity and is difficult to diagnose. Early diagnosis is essential for effective disease management. Kano G et al. (2016) Mol Med Reports
Approach:
- Identify individuals affected by syndrome using ultrastructural analysis of cilia
- Perform Ion AmpliSeq exome sequencing to identify variants
- Verify by Sanger sequencing
Results:
Identified two DNAH5 (dynein heavy chain 5) mutations:
- Mother was heterozygous for one allele (DNAH5 c.9101delG)
- Father was heterozygous for a different allele (DNAH5 c.5983C>T)
- Affected child had one of each of the defective alleles inherited from parents
About the technology
Human genetics research studies provide the disease-predisposing alleles that then feed into family planning screening tools. If two parents are both carriers of a recessive, disease-linked gene, then there is a 25% chance that their children will inherit the disease in question. Understanding the risk factors in different populations is the first stage in developing preventative medicine.
How best to identify hereditary conditions to prevent inheritance in the next generation?
Carrier screening
Carrier screening determines whether a healthy person possesses a copy of a disease-linked gene. The ideal carrier screening tool needs to incorporate all possible deleterious mutations that are found across ethnicities so that just a single test can be applied in every subject studied. This approach would cut down work, costs and multiple rounds of trial and error.
Approach:
- Select the most common variants from international populations in 600 disease-linked genes
- Design and verification process must enable high confidence and reproducibility in broad screening research
- Make it customisable so that researchers can study the widest range of populations possible and add new alleles as they are discovered
- Have a choice of automated or manual sample preparation
About the technology
Unravel the exome odyssey
Overcome the challenges of the exome odyssey with reliable single-exon deletion and duplication detection using the Applied Biosystems CytoScan XON Suite, for cost-effective and streamlined analysis of exon-level CNVs. Designed to cover the whole genome, with increased coverage in 7,000 clinically relevant genes, the CytoScan XON Suite provides CNV data that works as a strong complement to mutation analysis performed by next-generation sequencing (NGS).
Approach:
- Comprehensively detect single-exon deletions and duplications in a cost-effective manner
- Complement NGS mutation analysis with reliable exon-level deletion and duplication detection
- Confirm CNV findings from alternative technologies
- Simplify and streamline sequence variant analysis
About the technology
Genotyping continues to be an important molecular tool for precision medicine in the research and clinical setting. Study strategy has evolved rapidly in recent years, led by large population biobanks and precision medicine initiatives. Below, you can access the experience of leaders in the field on how they have solved the common genotyping challenges in complex trait genomics and pharmacogenomics.
What’s the most effective way to cover genomic variation in your population?
Learn how UK Biobank solved this challenge by reading this interview with Mark McCarthy, Robert Turner Professor of Diabetes at the University of Oxford and Consultant Endocrinologist at the Oxford University Hospitals Trust, Oxford, UK.
What is the best way to integrate genotyping into precision medicine studies?
In this webinar, Dr. Mark Bouzyk, Cofounder and Chief Scientific Officer of AKESOgen, USA, talks about his experience working on pharmacogenomics studies and the Million Veterans Program.
How will pharmacogenomics look in the future and what are the obstacles to getting there?
In this interview, Ulrich Broeckel, MD from Right Patient, Right Drug Diagnostics, USA discusses the value of and research into pre-emptive pharmacogenomics.
About the technology
Single-gene inheritance pattern (Mendelian disease)
See how you can quickly identify causative alleles in inherited diseases through candidate gene analysis using next generation sequencing of custom-assembled gene panels.
Molecular analysis of inherited cardiomyopathy using next generation semiconductor sequencing technologies - Chaoxia Lu et al
Approach:
- Identify causative variants of different inherited cardiomyopathies using a single Ion AmpliSeq gene panel.
- Perform targeted next-generation sequencing (NGS) on candidate genes.
- Verify genetic variants by Sanger sequencing.
Results:
- Potential pathogenic variants found in 23.6% of study samples, including a homozygous variant in the SLC25A4 gene.
- Of the pathogenic variants found, 15 had been reported in the Human Gene Mutation Database or ClinVar database, while 11 were novel.
- Most variants were found in MYH7 (8/26) and MYBPC3 (6/26) gene. Titin (TTN) truncating mutations account for 13% of the dilated cardiomyopathy cases (3/23).
About the technology
| For multiplex analysis of multiple genes, multiple samples for low cost variant detection: | |||
| | ||
| |||
| For single gene, single sample variant detection or NGS verification: | |||
| | ||
Multi-factorial (non-Mendelian) disease
Inherited diseases can also be caused by a combination of genetic loci which together result in potentially complex and variable phenotype, making disease identification more difficult. We show how a combination of chromosomal microarray analysis (CMA) and whole exome analysis (WES) can improve discovery rates over WES alone.
How can we identify non-Mendelian loci and quantify their contribution to disease?
Recent studies have shown that a combination of genomic array and sequential exome analysis, is an effective approach in the evaluation of subjects with unexplained intellectual disability, autism spectrum disorder and/or congenital anomalies. The expected clinical yield of these tests are for high resolution genomic array 15-20% and in combination with exome sequencing >50% (Vissers L et al. Nature Genetics, 2010, PMID: 21076407).
Example: Autism study
Molecular diagnostic yield of chromosomal microarray analysis and whole exome analysis using next-generation sequencing in children with autism spectrum disorder. Tammimies K et al. (2015) JAMA
Approach:
- Collect research samples from 258 unrelated children with Autistic Spectrum Disorder (ASD)
- Perform chromosomal microarray analysis (CMA)
- Perform whole exome sequencing (WES) on 100 probands, where DNA samples from both parents are available
Results:
- Of 258 probands, 24 identified pathogenic alleles from CMA and 8 of 95 from WES
- 96 de novo variants that could be contributive were also identified
About the technology
Non-familial congenital & germline disorders Reproductive health research Complex traits & pharmacogenomics
Trinucleotide repeat disorders
Incurable neurodegenerative diseases such as Huntington’s disease, spinocerebellar ataxias, fragile X syndrome, and SBMA are caused by unstable repetitive triplet elements within defined loci. Variability in repeat length is observed in normal alleles and can range from 15 to 40 nucleotides. Pathology results when repeat length exceeds a specific threshold, usually greater than 45. The disease phenotype may worsen from generation to generation due to de novo germline expansion of repeats.
How can we find disease-causing simple tandem repeat variants?
Example: Fragile X
More than 30 Mendelian disorders are linked to STR expansions. In Fragile X syndrome, tandem CGG repeats within the FMR1 gene are associated with onset and severity of frontotemporal dementia and amyotrophic lateral sclerosis.
Approach:
- The FMR1 CGG repeat region can range in size, and analysis of the gene requires resolution of long fragment lengths of 800bp or more
- Perform fragment sizing (fragment analysis) by capillary electrophoresis sequencing using the Applied Biosystems SeqStudio Genetic Analyzer and Asuragen AmplideX PCR/CE FMR1 and C9orf72 reagents
- Amplify the Asuragen AmplideX PCR/CE FMR1 and C9orf72 reagents from blood samples taken from Fragile X research subjects
- Run the AmplideX PCR/CE FMR1 and C9orf72 reagents under the following run parameters: SeqStudio module = LongFragAnalysis (modified), injection time = 2 sec, injection voltage = 6 kV, run time = 3,300 sec, and run voltage = 6 kV
- Run time takes around 30 minutes
Results:
- Consistent detection of expected n and n + 1 alleles demonstrates single-repeat assay resolution.
- Genotype and allele repeat lengths were 100% concordant with expected values.
About the technology
How do new mutations arise in families that don’t have a history of the disease?
How to find these causative mutations?
Example: Primary Ciliary Dyskinesia Case Study
A rare genetic disorder of ciliary function, affecting 1/20,000 live births, this disease has phenotypic heterogeneity and is difficult to diagnose. Early diagnosis is essential for effective disease management. Kano G et al. (2016) Mol Med Reports
Approach:
- Identify individuals affected by syndrome using ultrastructural analysis of cilia
- Perform Ion AmpliSeq exome sequencing to identify variants
- Verify by Sanger sequencing
Results:
Identified two DNAH5 (dynein heavy chain 5) mutations:
- Mother was heterozygous for one allele (DNAH5 c.9101delG)
- Father was heterozygous for a different allele (DNAH5 c.5983C>T)
- Affected child had one of each of the defective alleles inherited from parents
About the technology
Human genetics research studies provide the disease-predisposing alleles that then feed into family planning screening tools. If two parents are both carriers of a recessive, disease-linked gene, then there is a 25% chance that their children will inherit the disease in question. Understanding the risk factors in different populations is the first stage in developing preventative medicine.
How best to identify hereditary conditions to prevent inheritance in the next generation?
Carrier screening
Carrier screening determines whether a healthy person possesses a copy of a disease-linked gene. The ideal carrier screening tool needs to incorporate all possible deleterious mutations that are found across ethnicities so that just a single test can be applied in every subject studied. This approach would cut down work, costs and multiple rounds of trial and error.
Approach:
- Select the most common variants from international populations in 600 disease-linked genes
- Design and verification process must enable high confidence and reproducibility in broad screening research
- Make it customisable so that researchers can study the widest range of populations possible and add new alleles as they are discovered
- Have a choice of automated or manual sample preparation
About the technology
Unravel the exome odyssey
Overcome the challenges of the exome odyssey with reliable single-exon deletion and duplication detection using the Applied Biosystems CytoScan XON Suite, for cost-effective and streamlined analysis of exon-level CNVs. Designed to cover the whole genome, with increased coverage in 7,000 clinically relevant genes, the CytoScan XON Suite provides CNV data that works as a strong complement to mutation analysis performed by next-generation sequencing (NGS).
Approach:
- Comprehensively detect single-exon deletions and duplications in a cost-effective manner
- Complement NGS mutation analysis with reliable exon-level deletion and duplication detection
- Confirm CNV findings from alternative technologies
- Simplify and streamline sequence variant analysis
About the technology
Genotyping continues to be an important molecular tool for precision medicine in the research and clinical setting. Study strategy has evolved rapidly in recent years, led by large population biobanks and precision medicine initiatives. Below, you can access the experience of leaders in the field on how they have solved the common genotyping challenges in complex trait genomics and pharmacogenomics.
What’s the most effective way to cover genomic variation in your population?
Learn how UK Biobank solved this challenge by reading this interview with Mark McCarthy, Robert Turner Professor of Diabetes at the University of Oxford and Consultant Endocrinologist at the Oxford University Hospitals Trust, Oxford, UK.
What is the best way to integrate genotyping into precision medicine studies?
In this webinar, Dr. Mark Bouzyk, Cofounder and Chief Scientific Officer of AKESOgen, USA, talks about his experience working on pharmacogenomics studies and the Million Veterans Program.
How will pharmacogenomics look in the future and what are the obstacles to getting there?
In this interview, Ulrich Broeckel, MD from Right Patient, Right Drug Diagnostics, USA discusses the value of and research into pre-emptive pharmacogenomics.
About the technology
For Research Use Only. Not for use in diagnostic procedures.