Ignite Creation Date:
2024-05-06 @ 7:48 PM
Last Modification Date:
2024-10-26 @ 3:14 PM
Study NCT ID:
NCT06147414
Status:
NOT_YET_RECRUITING
Last Update Posted:
2024-02-28
First Post:
2023-09-18
Brief Title:
Development of Non-Invasive Prenatal Diagnosis for Single Gene Disorders
Sponsor:
Assistance Publique - Hôpitaux de Paris
Organization:
Assistance Publique - Hôpitaux de Paris
Study Overview
Official Title:
Evaluation of the Diagnostic Performance of Non-Invasive Prenatal Diagnosis for Single Gene Disorders
Status:
NOT_YET_RECRUITING
Status Verified Date:
2024-02
Last Known Status:
None
Delayed Posting:
No
If Stopped, Why?:
Not Stopped
Has Expanded Access:
False
If Expanded Access, NCT#:
N/A
Has Expanded Access, NCT# Status:
N/A
Acronym:
DANNIgene
Brief Summary:
Cell-free fetal DNA cffDNA is present in the maternal blood from the early first trimester of gestation and makes up 5-20 of the total circulating cell-free DNA cfDNA in maternal plasma Its presence in maternal plasma has allowed development of noninvasive prenatal diagnosis for single-gene disorders SGD-NIPD This can be performed from 9 weeks of amenorrhea and offers an early safe and accurate definitive diagnosis without the miscarriage risk associated with invasive procedures One of the major difficulties is distinguishing fetal genotype in the high background of maternal cfDNA which leads to several technical and analytical challenges Besides unlike noninvasive prenatal testing for aneuploidy NIPD for monogenic diseases represent a smaller market opportunity and many cases must be provided on a bespoke patient- or disease-specific basis As a result implementation of SGD-NIPD remained sparse with most testing being delivered in a research setting
The present project aims to take advantage of the unique French collaborative network to make SGD-NIPD possible for theoretically any monogenic disorder and any family
The present project aims to take advantage of the unique French collaborative network to make SGD-NIPD possible for theoretically any monogenic disorder and any family
Detailed Description:
Since the identification of cffDNA in maternal plasma in 1997 there have been rapid developments in exploiting its presence for prenatal diagnosis and screening The first proof of principle studies using cfDNA from maternal plasma to detect fetal aneuploidy were published in 2008 following which there was rapid commercialization Nowadays non-invasive prenatal testing NIPT for aneuploidies is widely used across the world as a screening test for the most frequent fetal trisomies Unlike non-invasive prenatal testing where a positive result requires confirmation following an invasive test non-invasive prenatal diagnosis NIPD offers the advantage of a definitive diagnosis without an invasive procedure - and its associated miscarriage risk - because confined placental mosaicism does not occur with NIPD for single-gene disorders SGD
NIPD can be offered earlier in pregnancy than invasive testing from 7 weeks of gestation This can reduce parental anxiety and allows more time for decision-making and planning Indeed there are substantial challenges to overcome for SGD-NIPD i Circulating cffDNA which is released from the placenta from about 4 weeks gestation makes up only 5-20 of total circulating cfDNA in maternal plasma This percentage increases with gestation and is influenced by factors such as maternal weight smoking and pregnancy complications such as preeclampsia Consequently optimized techniques and highly sensitive detection approaches are required to detect variants in the fetal DNA ii fetal fraction must be calculated to confirm that there are sufficient levels of cffDNA present and to avoid false negative results iii Another issue is the short fragment length of cffDNA which makes detection of triplet repeats and large deletions or duplications challenging
Besides fetal sex determination and fetal Rhesus D status principal investigators team was the first to propose SGD-NIPD for use in clinical practice in France for autosomal disorders caused by de novo or paternally inherited mutations for which variants in the fetal DNA can easily be distinguished in the high background of maternal cfDNA Droplet-digital Polymerase Chain Reaction or Next-Generation Sequencing can be used to target a single mutation for this analysis
However this approach requires mutation-specific developments and is restricted to point mutations that are absent from maternal DNA NIPD for X-linked disorders as well as autosomal dominant maternally inherited or autosomal recessive disorders for which both parents are carriers of the same mutation has posed a greater challenge A quantitative approach is needed to ascertain fetal inheritance of the maternal mutation In autosomal dominant diseases with maternal mutation or autosomal recessive diseases the ratio between the total copies of the mutant allele M and the wildtype allele N in the maternal plasma contributed by both the maternal and fetal cell-free DNA is expected to be balanced MN if the genotype of the fetus MN is identical to the mother MN However the allelic ratio will be imbalanced if the fetal genotype is different from the maternal genotype If the fetus has inherited both parental wildtype alleles NN there would be additional dosage of the wildtype allele in the maternal plasma contributed from the fetus resulting in under-representation in the total copies of the mutant allele MN Conversely if the fetus has inherited the parental mutant alleles MM there would be additional dosage of the mutant allele in the maternal plasma contributed from the fetus resulting in over-representation in the total copies of the mutant allele MN The degree of expected allelic imbalance in maternal plasma depends on the DNA fetal fraction in the maternal plasma
A quantitative relative mutation dosage RMD approach has been developed to detect such mutant allelic imbalance This approach has been applied to the non-invasive detection of recessive disorders such as beta-thalassemia and sickle cell anemia but also for X-linked disorders like hemophilia Nevertheless direct interrogation of the mutation appears to be difficult - even impossible - in certain genomic loci due to the presence of repetitive sequences homologous pseudogenes and undefined genomic rearrangement Moreover successful classification of allelic imbalance is statistically dependent on the available copies of mutant and wildtype alleles in the blood sample hampered by the very low absolute concentration of cfDNA As a result RMD analysis is still at a proof-of-concept phase being evaluated in a limited number of studies with a limited number of patients and has never been implemented in standard care diagnosis to investigators knowledge
These challenges have inspired an alternative solution with indirect mutational status inference by relative haplotype dosage analysis RHDO SGD-NIPD by indirect mutational status inference by RHDO has been shown to be successful for -thalassemia and is now in clinical practice only in the United Kingdom National Health Service for cystic fibrosis spinal muscular atrophy and Duchenne muscular dystrophy Although RHDO has been proven reliable quality controls and decisional thresholds are not thoroughly addressed for clinical implementation
Principal investigators team got inspired from the approach developed by Dennis Lo and enriched the methodological aspect i by comprehensively allowing to control the statistical errors ii by distinctly identifying key parameters that influence the diagnosis performance of RHDO iii by pinpointing output features illustrating the overall quality of the test
All these factors were then merged resulting in quality scores and decision threshold definition
A preliminary fruitful work involving more than 90 at risk families for 5 disorders was conducted by principal investigators team
Altogether the workflow appears to be
Specific 9292 100 fetal genotype correctly identified among conclusive tests ie 92 concordant 0 discordant results Sensitive 9298 94 conclusive tests among all tests ie 92 conclusive concordant results 6 inconclusive concordant results Clinically viable turn-around-time of 5-6 working days Universal applicable to any mutational profile point mutation deletion duplication triplet expansion etc
Adaptable can be easily modified for testing of other SGDs The present project aims to take advantage of the unique French collaborative network to make SGD-NIPD possible for theoretically any monogenic disorder and any family The investigators wish to build on this preliminary work to broaden the workflow to each disease of interest for a comprehensive evaluation of the diagnostic performance of SGD-NIPD Eventually this collaborative achievement will allow the redraw of French landscape of prenatal diagnosis
One advantage of the approach proposed in this study is that it is targeted The RHDO analysis and its result will be specific of DNA locus involved in the family disorder and will not affect other regions of the genome Consecutively investigators will not be confronted to ethical and social issues surrounding full exome or genome sequencing in the prenatal setting for example the counselling issues that arise through the identification of variants of uncertain significance or incidental findings
SGD-NIPD will be proposed by Multidisciplinary Centers for Prenatal Diagnosis to pregnant women undergoing invasive prenatal diagnosis in a context of family history of single-gene disorders because of parental pathogenic mutations in one of the following gene HBB CFTR FMR1 SMN1 DMPK DMD NF1 HTT F8 F9 GCK L1CAM PKHD1 or ATP7A
In the case of MODY-GCK diabetes fetal growth is dependent on fetal genotype Insulin treatment should be considered to reduce the risk of macrosomia only in the 50 of MODY-GCK mothers with unaffected foetus However invasive PND is not recommended in clinical care due to a significant benefitrisk imbalance For these MODY-GCK cases the result of the SGD-NIPD will be compared to the genotype result of the newborn at birth already planned as part of routine care The benefits of NIPD in the pregnancy management of women with pathogenic GCK variants has been demonstrated by international experts of monogenic diabetes
If the baby inherits the maternal GCK variant - the baby would be expected to have a normal birthweight as per background population
Treatment of maternal hyperglycemia is not recommended in those cases as the baby would not be expected to have a higher risk of being born large-for-gestational-age than the background population
However if the baby does not inherit the maternal GCK variant it would have a higher risk of macrosomia large-for-gestational-age 800g increase in birth weight Monitoring of fetal growth ultrasound 283236 weeks treatment for maternal hyperglycemia with insulin and planning delivery at 37-39 weeks gestation is recommended to try to limit fetal growth
Recruitment capacities are assessed by considering the prevalence of rare diseases and the activities of each co-investigator center as reported annually in the report of the biomedicine agency
NIPD can be offered earlier in pregnancy than invasive testing from 7 weeks of gestation This can reduce parental anxiety and allows more time for decision-making and planning Indeed there are substantial challenges to overcome for SGD-NIPD i Circulating cffDNA which is released from the placenta from about 4 weeks gestation makes up only 5-20 of total circulating cfDNA in maternal plasma This percentage increases with gestation and is influenced by factors such as maternal weight smoking and pregnancy complications such as preeclampsia Consequently optimized techniques and highly sensitive detection approaches are required to detect variants in the fetal DNA ii fetal fraction must be calculated to confirm that there are sufficient levels of cffDNA present and to avoid false negative results iii Another issue is the short fragment length of cffDNA which makes detection of triplet repeats and large deletions or duplications challenging
Besides fetal sex determination and fetal Rhesus D status principal investigators team was the first to propose SGD-NIPD for use in clinical practice in France for autosomal disorders caused by de novo or paternally inherited mutations for which variants in the fetal DNA can easily be distinguished in the high background of maternal cfDNA Droplet-digital Polymerase Chain Reaction or Next-Generation Sequencing can be used to target a single mutation for this analysis
However this approach requires mutation-specific developments and is restricted to point mutations that are absent from maternal DNA NIPD for X-linked disorders as well as autosomal dominant maternally inherited or autosomal recessive disorders for which both parents are carriers of the same mutation has posed a greater challenge A quantitative approach is needed to ascertain fetal inheritance of the maternal mutation In autosomal dominant diseases with maternal mutation or autosomal recessive diseases the ratio between the total copies of the mutant allele M and the wildtype allele N in the maternal plasma contributed by both the maternal and fetal cell-free DNA is expected to be balanced MN if the genotype of the fetus MN is identical to the mother MN However the allelic ratio will be imbalanced if the fetal genotype is different from the maternal genotype If the fetus has inherited both parental wildtype alleles NN there would be additional dosage of the wildtype allele in the maternal plasma contributed from the fetus resulting in under-representation in the total copies of the mutant allele MN Conversely if the fetus has inherited the parental mutant alleles MM there would be additional dosage of the mutant allele in the maternal plasma contributed from the fetus resulting in over-representation in the total copies of the mutant allele MN The degree of expected allelic imbalance in maternal plasma depends on the DNA fetal fraction in the maternal plasma
A quantitative relative mutation dosage RMD approach has been developed to detect such mutant allelic imbalance This approach has been applied to the non-invasive detection of recessive disorders such as beta-thalassemia and sickle cell anemia but also for X-linked disorders like hemophilia Nevertheless direct interrogation of the mutation appears to be difficult - even impossible - in certain genomic loci due to the presence of repetitive sequences homologous pseudogenes and undefined genomic rearrangement Moreover successful classification of allelic imbalance is statistically dependent on the available copies of mutant and wildtype alleles in the blood sample hampered by the very low absolute concentration of cfDNA As a result RMD analysis is still at a proof-of-concept phase being evaluated in a limited number of studies with a limited number of patients and has never been implemented in standard care diagnosis to investigators knowledge
These challenges have inspired an alternative solution with indirect mutational status inference by relative haplotype dosage analysis RHDO SGD-NIPD by indirect mutational status inference by RHDO has been shown to be successful for -thalassemia and is now in clinical practice only in the United Kingdom National Health Service for cystic fibrosis spinal muscular atrophy and Duchenne muscular dystrophy Although RHDO has been proven reliable quality controls and decisional thresholds are not thoroughly addressed for clinical implementation
Principal investigators team got inspired from the approach developed by Dennis Lo and enriched the methodological aspect i by comprehensively allowing to control the statistical errors ii by distinctly identifying key parameters that influence the diagnosis performance of RHDO iii by pinpointing output features illustrating the overall quality of the test
All these factors were then merged resulting in quality scores and decision threshold definition
A preliminary fruitful work involving more than 90 at risk families for 5 disorders was conducted by principal investigators team
Altogether the workflow appears to be
Specific 9292 100 fetal genotype correctly identified among conclusive tests ie 92 concordant 0 discordant results Sensitive 9298 94 conclusive tests among all tests ie 92 conclusive concordant results 6 inconclusive concordant results Clinically viable turn-around-time of 5-6 working days Universal applicable to any mutational profile point mutation deletion duplication triplet expansion etc
Adaptable can be easily modified for testing of other SGDs The present project aims to take advantage of the unique French collaborative network to make SGD-NIPD possible for theoretically any monogenic disorder and any family The investigators wish to build on this preliminary work to broaden the workflow to each disease of interest for a comprehensive evaluation of the diagnostic performance of SGD-NIPD Eventually this collaborative achievement will allow the redraw of French landscape of prenatal diagnosis
One advantage of the approach proposed in this study is that it is targeted The RHDO analysis and its result will be specific of DNA locus involved in the family disorder and will not affect other regions of the genome Consecutively investigators will not be confronted to ethical and social issues surrounding full exome or genome sequencing in the prenatal setting for example the counselling issues that arise through the identification of variants of uncertain significance or incidental findings
SGD-NIPD will be proposed by Multidisciplinary Centers for Prenatal Diagnosis to pregnant women undergoing invasive prenatal diagnosis in a context of family history of single-gene disorders because of parental pathogenic mutations in one of the following gene HBB CFTR FMR1 SMN1 DMPK DMD NF1 HTT F8 F9 GCK L1CAM PKHD1 or ATP7A
In the case of MODY-GCK diabetes fetal growth is dependent on fetal genotype Insulin treatment should be considered to reduce the risk of macrosomia only in the 50 of MODY-GCK mothers with unaffected foetus However invasive PND is not recommended in clinical care due to a significant benefitrisk imbalance For these MODY-GCK cases the result of the SGD-NIPD will be compared to the genotype result of the newborn at birth already planned as part of routine care The benefits of NIPD in the pregnancy management of women with pathogenic GCK variants has been demonstrated by international experts of monogenic diabetes
If the baby inherits the maternal GCK variant - the baby would be expected to have a normal birthweight as per background population
Treatment of maternal hyperglycemia is not recommended in those cases as the baby would not be expected to have a higher risk of being born large-for-gestational-age than the background population
However if the baby does not inherit the maternal GCK variant it would have a higher risk of macrosomia large-for-gestational-age 800g increase in birth weight Monitoring of fetal growth ultrasound 283236 weeks treatment for maternal hyperglycemia with insulin and planning delivery at 37-39 weeks gestation is recommended to try to limit fetal growth
Recruitment capacities are assessed by considering the prevalence of rare diseases and the activities of each co-investigator center as reported annually in the report of the biomedicine agency
Study Oversight
Has Oversight DMC:
None
Is a FDA Regulated Drug?:
False
Is a FDA Regulated Device?:
False
Is an Unapproved Device?:
None
Is a PPSD?:
None
Is a US Export?:
None
Is an FDA AA801 Violation?:
None
Secondary IDs
| Secondary ID | Type | Domain | Link |
|---|---|---|---|
| 2023-A00821-44 | OTHER | ID-RCB | None |