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Embryo Developmental Arrest – 38 genes

Embryo Developmental Arrest (EDA) is one of the mechanisms responsible for an increased level of embryo demise during the first week of in vitro development. 
Overview
Indication
Clinical Utility
Genes & Diseases
Methodology
References

Overview

  • Embryo Developmental Arrest (EDA) is one of the mechanisms responsible for an increased level of embryo demise during the first week of in vitro development. Around 10-15% embryos permanently arrest in mitosis at the 2-to 4-cell cleavage stage. It involves the downregulation and/or cessation of cell division and metabolic activity of the components involved in the formation and development of an embryo. 

  • Chromosomal abnormalities, abnormal preimplantation development and single gene disorders have been stated as causes of EDA and therefore, a known cause of infertility. The identification of abnormal gene changes previously known to have an effect on embryo development is crucial to improve pregnancy outcomes.  

  • The Igenomix Embryo Developmental Arrest Precision Panel can be used to make a directed and accurate differential diagnosis of inability to carry out a full pregnancy ultimately leading to a better management and achieve a healthy baby at home. It provides a comprehensive analysis of the genes involved in this disease using next-generation sequencing (NGS) to fully understand the spectrum of relevant genes involved.  

Indication

The Igenomix Infertility Precision Panel is indicated for those patients with clinical suspicion of infertility presenting with the following manifestations: 

  • Inability to conceive after 1 year of unprotected intercourse  
  • Family history of infertility  
  • Personal or family history of recurrent miscarriages  
  • Previous failed IVF cycles 
  • Other failed assisted reproductive technology (ART) treatments 

Clinical Utility

The clinical utility of this panel is: 

  • The genetic and molecular confirmation for an accurate clinical diagnosis of a symptomatic patient.  
  • Early initiation of treatment with a multidisciplinary team for an initial consultation, workup and assisted reproductive technologies (ART). 
  • Risk assessment of asymptomatic family members according to the mode of inheritance. 

Genes & Diseases

All genes and diseases
Gene OMIM DISEASES Inheritance* % Gene Coverage (20x) HGMD**
ABCD4 Methylmalonic Aciduria And Homocystinuria AR 100 8 of 8
ACTA2 Multisystemic Smooth Muscle Dysfunction Syndrome AD 100 88 of 88
ACTC1 Atrial Septal Defect, Left Ventricular Noncompaction, Familial Hypertrophic Cardiomyopathy, Familial Isolated Dilated Cardiomyopathy AD 99.93 72 of 74
ACVRL1 Osler-Rendu-Weber Syndrome AD 100 457 of 462
AFF4 CHOPS Syndrome, Short Stature-Skeletal Dysplasia Syndrome AD 99.42 6 of 6
ALMS1 Alstrom Syndrome AR 99.92 302 of 305
ARHGAP31 Adams-Oliver Syndrome AD 100 6 of 6
ATP5F1A Combined Oxidative Phosphorylation Deficiency, Mitochondrial Complex V (ATP Synthase) Deficiency AR 91.8 NA of NA
BANF1 Nestor-Guillermo Progeria Syndrome AR 100 1 of 1
BMPR2 Primary Pulmonary Hypertension, Pulmonary Venoocclusive Disease AD 99.99 590 of 600
BTNL2 Sarcoidosis AD 99.98 1 of 1
CACNA1D Primary Aldosteronism, Seizures, And Neurologic Abnormalities, Sinoatrial Node Dysfunction And Deafness AD,AR 100 18 of 18
CAV1 Primary Pulmonary Hypertension, Diffuse Cutaneous Systemic Sclerosis , Limited Cutaneous Systemic Sclerosis AD,AR 100 18 of 18
CCN2 Diffuse Cutaneous Systemic Sclerosis, Limited Cutaneous Systemic Sclerosis – 95.83 NA of NA
CCR6 Diffuse Cutaneous Systemic Sclerosis, Limited Cutaneous Systemic Sclerosis – 99.83 NA of NA
CHST3 Multiple Joint Dislocations, Short Stature, Craniofacial Dysmorphism, With Or Without Congenital Heart Defects AR 99.97 38 of 38
CITED2 Atrial Septal Defect , Ventricular Septal Defect,Tetralogy Of Fallot AD 99.22 18 of 24
CLCN7 Hypopigmentation, Organomegaly, And Delayed Myelination And Development, Albers-Schonberg Osteopetrosis AD,AR 99.85 109 of 111
COG1 Congenital Disorder Of Glycosylation Type IIg AR 99.91 3 of 3
COL1A1 Caffey Disease , Ehlers-danlos Syndrome Type VII, Arthrochalasia Ehlers-Danlos Syndrome AD 99.98 1156 of 1159
COL1A2 Ehlers-Danlos Syndrome Arthrochalasia Type, Cardiac-Valvular Ehlers-Danlos Syndrome AD,AR 100 576 of 581
COLQ Synaptic Congenital Myasthenic Syndromes AR 100 70 of 71
COX1 Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes, Leber Hereditary Optic Neuropathy MI na na
COX2 Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes MI na na
COX3 Leber Optic Atrophy , Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes , Leber Hereditary Optic Neuropathy MI na na
COX7B Aplasia Cutis Congenita, Reticulolinear, With Microcephaly, Facial Dysmorphism, And Other Congenital Anomalies X,XD,G 99.97 NA of NA
CTCF Intellectual Disability-Feeding Difficulties-Developmental Delay-Microcephaly Syndrome AD 96.6 39 of 41
DLL4 Adams-Oliver Syndrome AD 99.98 21 of 21
DOCK6 Adams-oliver Syndrome AR 98.06 37 of 37
EIF2AK4 Pulmonary Venoocclusive Disease AR 99.98 102 of 102
ENG Hereditary Hemorrhagic Telangiectasia, Generalized Juvenile Polyposis/Juvenile Polyposis Coli AD 100 467 of 471
EOGT Adams-oliver Syndrome AR 100 11 of 11
FBN1 Marfan Lipodystrophy Syndrome, Mass Syndrome, Stiff Skin Syndrome, Weill-Marchesani Syndrome, Neonatal Marfan Syndrome, Shprintzen-Goldberg Syndrome AD 100 2836 of 2845
FGFR1 Hartsfield Syndrome, Jackson-Weiss Syndrome, Pfeiffer Syndrome, Hartsfield Syndrome AD 100 279 of 280
FGFR3 Crouzon Syndrome With Acanthosis Nigricans, Muenke Syndrome, Camptodactyly-Tall Stature-Scoliosis-Hearing Loss Syndrome, Crouzon Syndrome-Acanthosis Nigricans Syndrome, Saethre-Chotzen Syndrome AD,AR 99.89 77 of 78
FIG4 Amyotrophic Lateral Sclerosis, Charcot-Marie-Tooth Disease, Yunis-Varon Syndrome AD,AR 99.92 72 of 72
FLNA Cardiac Valvular Dysplasia, Melnick-Needles Syndrome, X-linked Ehlers-Danlos Syndrome X,XR,XD,G 100 NA of NA
FLNC Familial Hypertrophic Cardiomyopathy, Filaminopathy, Distal Myopathy, Familial Isolated Restrictive Cardiomyopathy AD 100 185 of 186
FOXF1 Alveolar Capillary Dysplasia With Misalignment Of Pulmonary Veins , Congenital Alveolar Capillary Dysplasia AD 95.93 74 of 96
FOXP1 Mental Retardation With Language Impairment And With Or Without Autistic Features, Intellectual Disability-Severe Speech Delay-Mild Dysmorphism Syndrome AD 100 63 of 80
G6PC3 Severe Congenital Neutropenia AR 100 45 of 45
GATA4 Atrial Septal Defect, Atrioventricular Septal Defect, Testicular Anomalies With Or Without Congenital Heart Disease, Tetralogy Of Fallot, Ventricular Septal Defect AD 94.69 108 of 130
GATA6 Atrial Septal Defect, Atrioventricular Septal Defect, Conotruncal Heart Malformations, Truncus Arteriosus Communis, Pancreatic Agenesis And Congenital Heart Defects, Tetralogy Of Fallot, Congenital Diaphragmatic Hernia Syndrome AD,AR 84.19 66 of 84
GBA Gaucher Disease, Gaucher Disease-Ophthalmoplegia-Cardiovascular Calcification Syndrome AD,AR 100 469 of 471
GDF2 Hereditary Hemorrhagic Telangiectasia AD 98.58 51 of 57
GJA1 Atrioventricular Septal Defect, Hypoplastic Left Heart Syndrome AD,AR,MU,O 100 119 of 119
HBB Alpha-Thalassemia, Beta-Thalassemia, Sickle Cell Anemia, Delta-Beta-Thalassemia, Hemoglobin C-Beta-Thalassemia Syndrome, Hemoglobin E-Beta-Thalassemia Syndrome AD,AR 100 753 of 789
HLA-B Spondyloarthropathy, Behcet Disease, Takayasu Arteritis MU 99.55 1 of 1
HLA-DRB1 Multiple Sclerosis, Sarcoidosis, Diffuse Cutaneous Systemic Sclerosis, Limited Cutaneous Systemic Sclerosis AD,MU 97.19 2 of 2
HSPG2 Dyssegmental Dysplasia Silverman-Handmaker Type , Schwartz-Jampel Syndrome Type 1 AR 99.41 68 of 69
IDUA Hurler Syndrome, Hurler-Scheie Syndrome AR 99.73 287 of 292
IKBKG Ectodermal Dysplasia And Immunodeficiency X,XR,XD,G 38.16 NA of NA
IL12B Immunodeficiency, Takayasu Arteritis AR 100 12 of 12
IRF5 Diffuse Cutaneous Systemic Sclerosis, Limited Cutaneous Systemic Sclerosis, Primary Biliary Cholangitis – 99.33 1 of 1
JAK2 Budd-Chiari Syndrome, Familial Erythrocytosis, Myelofibrosis With Myeloid Metaplasia, Polycythemia Vera, Essential Thrombocythemia, Primary Myelofibrosis AD,AR 99.63 25 of 27
KCNK3 Primary Pulmonary Hypertension AD 98.11 23 of 26
KCNN4 Dehydrated Hereditary Stomatocytosis AD 99.78 3 of 4
KIAA0319L Limited Cutaneous Systemic Sclerosis – 99.97 NA of NA
KIF20A Familial Isolated Restrictive Cardiomyopathy – 99.97 2 of 2
KRAS Cardiofaciocutaneous Syndrome, Noonan Syndrome, Pancreatic Cancer, Schimmelpenning-Feuerstein-Mims Syndrome, Toriello-Lacassie-Droste Syndrome AD 100 38 of 38
KRT18 Familial Cirrhosis With Pulmonary Hypertension AD,AR 100 14 of 14
KRT8 Familial Cirrhosis With Pulmonary Hypertension AD,AR 99.98 26 of 26
LAMA2 Muscular Dystrophy, Congenital Merosin-Deficient 1a, Limb-Girdle Muscular Dystrophy, Laminin Subunit Alpha 2-Related Congenital Muscular Dystrophy AR 100 363 of 377
LAMB2 Pierson Syndrome, Synaptic Congenital Myasthenic Syndromes AR 100 129 of 129
LIFR Stuve-Wiedemann Syndrome AR 99.81 33 of 33
LIPA Lysosomal Acid Lipase Deficiency, Cholesteryl Ester Storage Disease, Wolman Disease AR 99.91 103 of 104
LIPT1 Lipoyl Transferase Deficiency, Leigh Syndrome With Leukodystrophy AR 97.25 10 of 10
LMNA Dilated Cardiomyopathy, Charcot-Marie-Tooth Disease Type 2b1, Emery-Dreifuss Muscular Dystrophy, Heart-Hand Syndrome, Hutchinson-Gilford Progeria Syndrome, Malouf Syndrome, Lethal Restrictive Dermopathy AD,AR 100 619 of 620
MED12 Lujan-Fryns Syndrome, Ohdo Syndrome, Opitz-Kaveggia Syndrome, X-linked Intellectual Disability With Marfanoid Habitus X,XR,G 100 NA of NA
MED25 Basel-Vanagaite-Smirin-Yosef Syndrome, Charcot-Marie-Tooth Disease Type 2b2 AR 100 5 of 5
MGP Keutel Syndrome AR 99.93 7 of 7
MLX Takayasu Arteritis 82.12 NA of NA
MPL Myelofibrosis With Myeloid Metaplasia, Essential Thrombocythemia, Familial Thrombocytosis, Polycythemia Vera, Primary Myelofibrosis AD,AR 100 55 of 55
MUC5B Idiopathic Pulmonary Fibrosis AD 99.89 12 of 12
MYH6 Atrial Septal Defect, Dilated Cardiomyopathy, Familial Hypertrophic Cardiomyopathy AD 99.94 140 of 142
MYPN Dilated Cardiomyopathy, Familial Hypertrophic Cardiomyopathy, Nemaline Myopathy, Cap Myopathy, Familial Isolated Restrictive Cardiomyopathy AD,AR 99.94 49 of 49
ND1 Leber Optic Atrophy, Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes, Leber Hereditary Optic Neuropathy, Mitochondrial DNA-Associated Leigh Syndrome MI na na
ND4 Leber Optic Atrophy, Leber Hereditary Optic Neuropathy, Mitochondrial DNA-Associated Leigh Syndrome MI na na
ND5 Leber Optic Atrophy, Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes, Leber Hereditary Optic Neuropathy, Mitochondrial DNA-Associated Leigh Syndrome MI 99.89 NA of NA
ND6 Leber Optic Atrophy , Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes, Leber Hereditary Optic Neuropathy, Mitochondrial DNA-Associated Leigh Syndrome MI 100 NA of NA
NFIX Marshall-Smith Syndrome, Sotos Syndrome, Malan Overgrowth Syndrome, Marshall-Smith Syndrome AD 94.42 75 of 81
NFU1 Multiple Mitochondrial Dysfunctions Syndrome AR 100 13 of 15
NKX2-1 Choreoathetosis, Hypothyroidism, And Neonatal Respiratory Distress, Brain-Lung-Thyroid Syndrome AD 97.04 115 of 123
NKX2-5 Atrial Septal Defect With Or Without Atrioventricular Conduction Defects, Conotruncal Heart Malformations, Truncus Arteriosus Communis, Hypoplastic Left Heart Syndrome, Tetralogy Of Fallot, Ventricular Septal Defect, Atrial Septal Defect, Familial Bicuspid Aortic Valve, Familial Progressive Cardiac Conduction Defect, Hypoplastic Left Heart Syndrome, Tetralogy Of Fallot AD,AR 99.98 112 of 116
NOD2 Inflammatory Bowel Disease, Yao Syndrome, Blau Syndrome AD,MU 100 97 of 97
NOTCH1 Adams-Oliver Syndrome, Aortic Valve Disease, Familial Bicuspid Aortic Valve AD 99.83 178 of 179
PAM16 Chondrodysplasia, Megarbane-Dagher-Melki Type AR 41 2 of 2
PDSS1 Coenzyme Q10 Deficiency AR 97.34 5 of 5
PIEZO1 Dehydrated Hereditary Stomatocytosis AD,AR 99.98 107 of 107
PIGA Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome, Paroxysmal Nocturnal Hemoglobinuria, West Syndrome X,XR,G 97.98 NA of NA
PIGN Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome, Fryns Syndrome AR 93.97 36 of 39
PPCS Dilated Cardiomyopathy AR 98.95 4 of 4
RBPJ Adams-Oliver Syndrome AD 99.98 8 of 8
SARS2 Hyperuricemia, Pulmonary Hypertension, Renal Failure, And Alkalosis AR 97.5 6 of 6
SCARB2 Action Myoclonus-Renal Failure Syndrome, Gaucher Disease, Unverricht-Lundborg Disease AR 99.95 29 of 29
SFTPA2 Idiopathic Pulmonary Fibrosis AD 99.98 6 of 6
SFTPB Pulmonary Surfactant Metabolism Dysfunction, Infant Acute Respiratory Distress Syndrome, Neonatal Acute Respiratory Distress Due To Sp-b Deficiency AR 100 27 of 27
SFTPC Idiopathic Pulmonary Fibrosis, Surfactant Metabolism Dysfunction, Infant Acute Respiratory Distress Syndrome AD 99.84 83 of 83
SLC25A24 Fontaine Progeroid Syndrome, Gorlin-Chaudhry-Moss Syndrome AD 99.59 2 of 2
SLC29A3 Histiocytosis-Lymphadenopathy Plus Syndrome, Dysosteosclerosis AR 100 32 of 32
SLC37A4 Glycogen Storage Disease Ib, Glycogen Storage Disease Ic AR 99.97 112 of 112
SLC4A1 Hereditary Spherocytosis, Dehydrated Hereditary Stomatocytosis AD,AR 100 139 of 139
SMAD4 Juvenile Polyposis Syndrome, Hereditary Hemorrhagic Telangiectasia, Myhre Syndrome AD 99.56 136 of 136
SMAD9 Primary Pulmonary Hypertension AD 99.97 35 of 35
SNX10 Osteopetrosis AR 100 14 of 14
SPECC1L Opitz Gbbb Syndrome AD 99.66 14 of 14
STAT1 Immunodeficiency, Mycobacterial And Viral Infections, Autoimmune Enteropathy And Endocrinopathy-Susceptibility To Chronic Infections Syndrome AD,AR 100 138 of 138
TBX20 Atrial Septal Defect Ostium Secundum Type AD 99.98 33 of 34
TBX4 Ischiocoxopodopatellar Syndrome With Or Without Pulmonary Arterial Hypertension, Coxopodopatellar Syndrome AD,AR 99.72 91 of 94
TCIRG1 Osteopetrosis, Autosomal Dominant Severe Congenital Neutropenia, Dysosteosclerosis AR 100 140 of 146
TERT Pulmonary Fibrosis And/Or Bone Marrow Failure, Telomere-Related, Idiopathic Pulmonary Fibrosis, Hoyeraal-Hreidarsson Syndrome AD,AR 99.09 194 of 197
THPO Thrombocythemia, Familial Thrombocytosis AD 100 11 of 11
TLL1 Atrial Septal Defect Ostium Primum Type , Atrial Septal Defect Ostium Secundum Type AD 99.96 8 of 8
TNFSF11 Osteopetrosis AR 99.84 4 of 4
TNNI3 Dilated Cardiomyopathy, Familial Hypertrophic Cardiomyopathy, Familial Restrictive Cardiomyopathy AD,AR 100 139 of 139
TNNT2 Dilated Cardiomyopathy, Familial Hypertrophic Cardiomyopathy, Familial Restrictive Cardiomyopathy AD 100 169 of 169
TRNF Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes, Myoclonic Epilepsy Associated With Ragged-Red Fibers MI NA NA
TRNH Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes, Myoclonic Epilepsy Associated With Ragged-Red Fibers – NA NA
TRNL1 Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes, Myoclonic Epilepsy Associated With Ragged-Red Fibers, Kearns-Sayre Syndrome, Mitochondrial DNA-Associated Leigh Syndrome MI NA NA
TRNQ Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes MI NA NA
TRNS1 Mitochondrial Complex IV Deficiency , Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes , Mitochondrial DNA-Related Progressive External Ophthalmoplegia AR,MI NA NA
TRNS2 Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes, Usher Syndrome Type 3 MI NA NA
TRNW Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, And Stroke-Like Episodes , Mitochondrial Myopathy, Episodic, With Optic Atrophy And Reversible Leukoencephalopathy , Mitochondrial DNA-associated Leigh Syndrome AR,MI NA NA
UBE2A Mental Retardation, X-linked, Syndromic, Nascimento Type X,XR,G 99.99 NA of NA
VAC14 Striatonigral Degeneration, Childhood-Onset, Yunis-Varon Syndrome AR 100 11 of 11
VPS33A Mucopolysaccharidosis-Like Syndrome With Congenital Heart Defects And Hematopoietic Disorders AR 97.86 1 of 1
ZMPSTE24 Mandibuloacral Dysplasia With Type B Lipodystrophy, Lethal Restrictive Dermopathy, Hutchinson-Gilford Progeria Syndrome AR 100 35 of 36

* Inheritance: AD: Autosomal Dominant; AR: Autosomal Recessive; X: X linked; XLR: X linked Recessive; Mi: Mitochondrial; Mu: Multifactorial; G: Gonosomal Inheritance; D: Digenic Inheritance 

** HGMD: Number of clinically relevant mutations according to HGMD

Methodology

References

See scientific referrals

Murphy, B. (2020). Under Arrest: The Embryo in Diapause. Developmental Cell, 52(2), 139-140. doi: 10.1016/j.devcel.2020.01.002 

Levy, R. R., Cordonier, H., Czyba, J. C., & Guerin, J. F. (2001). Apoptosis in preimplantation mammalian embryo and genetics. Italian journal of anatomy and embryology = Archivio italiano di anatomia ed embriologia, 106(2 Suppl 2), 101–108. 

Mohebi, M., & Ghafouri-Fard, S. (2019). Embryo developmental arrest: Review of genetic factors and pathways. Gene Reports, 17, 100479. doi: 10.1016/j.genrep.2019.100479 

Zhang, X., Stojkovic, P., Przyborski, S., Cooke, M., Armstrong, L., Lako, M., & Stojkovic, M. (2006). Derivation of Human Embryonic Stem Cells from Developing and Arrested Embryos. Stem Cells, 24(12), 2669-2676. doi: 10.1634/stemcells.2006-0377 

Sha, Q. Q., Zheng, W., Wu, Y. W., Li, S., Guo, L., Zhang, S., Lin, G., Ou, X. H., & Fan, H. Y. (2020). Dynamics and clinical relevance of maternal mRNA clearance during the oocyte-to-embryo transition in humans. Nature communications, 11(1), 4917. https://doi.org/10.1038/s41467-020-18680-6 

Zhang, Y., Feng, Y., & Ma, F. (2020). Yi chuan = Hereditas, 42(10), 1004–1016. https://doi.org/10.16288/j.yczz.20-144 

Feng, R., Yan, Z., Li, B., Yu, M., Sang, Q., Tian, G., Xu, Y., Chen, B., Qu, R., Sun, Z., Sun, X., Jin, L., He, L., Kuang, Y., Cowan, N. J., & Wang, L. (2016). Mutations in TUBB8 cause a multiplicity of phenotypes in human oocytes and early embryos. Journal of medical genetics, 53(10), 662–671. https://doi.org/10.1136/jmedgenet-2016-103891 

Xu, Y., Shi, Y., Fu, J., Yu, M., Feng, R., & Sang, Q. et al. (2016). Mutations in PADI6 Cause Female Infertility Characterized by Early Embryonic Arrest. The American Journal Of Human Genetics, 99(3), 744-752. doi: 10.1016/j.ajhg.2016.06.024 

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