AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data

Quinodoz, Mathieu; Peter, Virginie G.; Bedoni, Nicola; Bertrand, Béryl Royer; Cisarova, Katarina; Salmaninejad, Arash; Sepahi, Neda; Rodrigues, Renata; Piran, Mehran; Mojarrad, Majid; Pasdar, Alireza; Asad, Ali Ghanbari; Sousa, Ana Berta; Coutinho-Santos, Luísa; Superti‐Furga, Andrea; Rivolta, Carlo

doi:10.1038/s41467-020-20584-4

Cited by 88 publications

(77 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…AutoMap, for example, was conducted and tested to be one of the best homozygosity mapping tools by a similar recent study in Iranian families. With AutoMap, the researchers predicted ROHs from WES data with high specificity and sensitivity, and also obtain a high detection rate in their IRD cohort [ 56 ]. De novo mutations should arouse great attention and whole genome sequencing (WGS) and long-read sequencing can play reliable roles in detecting large structural variations.…”

Section: Discussionmentioning

confidence: 99%

Consanguinity-based analysis of exome sequencing yields likely genetic causes in patients with inherited retinal dystrophy

Shen

Wang

et al. 2021

Orphanet J Rare Dis

View full text Add to dashboard Cite

Background Consanguineous families have a relatively high prevalence of genetic disorders caused by bi-allelic mutations in recessive genes. This study aims to evaluate the effectiveness and efficiency of a consanguinity-based exome sequencing approach to capturing genetic mutations in inherited retinal dystrophy families with consanguineous marriages. Methods Ten unrelated consanguineous families with a proband affected by inherited retinal dystrophy were recruited in this study. All participants underwent comprehensive ophthalmic examinations. Whole exome sequencing was performed, followed by a homozygote-prior strategy to rapidly filter disease-causing mutations. Bioinformatic prediction of pathogenicity, Sanger sequencing and co-segregation analysis were carried out for further validation. Results In ten consanguineous families, a total of 10 homozygous mutations in 8 IRD genes were identified, including 2 novel mutations, c.1654_1655delAG (p. R552Afs*5) in gene FAM161A in a patient diagnosed with retinitis pigmentosa, and c.830T > C (p.L277P) in gene CEP78 in a patient diagnosed with cone and rod dystrophy. Conclusion The genetic etiology in consanguineous families with IRD were successfully identified using consanguinity-based analysis of exome sequencing data, suggesting that this approach could provide complementary insights into genetic diagnoses in consanguineous families with variant genetic disorders.

show abstract

Section: Discussionmentioning

confidence: 99%

Consanguinity-based analysis of exome sequencing yields likely genetic causes in patients with inherited retinal dystrophy

Shen

Wang

et al. 2021

Orphanet J Rare Dis

View full text Add to dashboard Cite

show abstract

“…We ran a omozygosity plot on patient 2 using AutoMap ( Quinodoz et al, 2021 ). The Runs of Homozygosity (ROH) region in patient 2 was 43.13 Mb in total ( Supplementary Figure 2 ).…”

Section: Discussionmentioning

confidence: 99%

Rapid Trio Exome Sequencing for Autosomal Recessive Renal Tubular Dysgenesis in Recurrent Oligohydramnios

et al. 2021

View full text Add to dashboard Cite

Oligohydramnios is not a rare prenatal finding. However, recurrent oligohydramnios is uncommon, and genetic etiology should be taken into consideration. We present two families with recurrent fetal oligohydramnios that did not respond to amnioinfusion. Rapid trio-whole-exome sequencing (WES) revealed mutations in the AGT gene in both families within 1 week. The first family had a compound heterozygous mutation with c.856 + 1G > T and c.857-619_1269 + 243delinsTTGCCTTGC changes. The second family had homozygous c.857-619_1269 + 243delinsTTGCCTTGC mutations. AGT gene mutation may lead to autosomal recessive renal tubular dysgenesis, a rare and lethal disorder that can result in early neonatal death. Both the alleles identified are known alleles associated with pathogenicity. Our findings suggest that trio-WES analysis may help rapidly identify causative etiologies that can inform prompt counseling and decision-making prenatally.

show abstract

“…Homozygous and hemizygous variants with a MAF < 1% in the general population (1000genome, EVS, gnomAD) were retained and screened for variants in reported ID genes (Supplementary Table 1). Homozygosity mapping was performed with AutoMap, which uses Variant Call Format (VCF) files from WES 60 .…”

Section: Methodsmentioning

confidence: 99%

Biallelic truncation variants in ATP9A are associated with a novel autosomal recessive neurodevelopmental disorder

Mattioli

Darvish

Paracha

et al. 2021

Preprint

View full text Add to dashboard Cite

Intellectual disability (ID) is a highly heterogeneous disorder with hundreds of associated genes. Despite progress in the identification of the genetic causes of ID following the introduction of high-throughput sequencing, about half of affected individuals still remain without a molecular diagnosis. Consanguineous families with affected individuals provide a unique opportunity to identify novel recessive causative genes. In this report we describe a novel autosomal recessive neurodevelopmental disorder. We identified two consanguineous families with homozygous variants predicted to alter the splicing of ATP9A which encodes a transmembrane lipid flippase of the class II P4-ATPases. The three individuals homozygous for these putatively truncating variants presented with severe ID, motor and speech impairment, and behavioral anomalies. Consistent with a causative role of ATP9A in these patients, a previously described Atp9a-/- mouse model showed behavioral changes.

show abstract

AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data

Cited by 88 publications

References 39 publications

Consanguinity-based analysis of exome sequencing yields likely genetic causes in patients with inherited retinal dystrophy

Consanguinity-based analysis of exome sequencing yields likely genetic causes in patients with inherited retinal dystrophy

Rapid Trio Exome Sequencing for Autosomal Recessive Renal Tubular Dysgenesis in Recurrent Oligohydramnios

Biallelic truncation variants in ATP9A are associated with a novel autosomal recessive neurodevelopmental disorder

Contact Info

Product

Resources

About