Browsing by Author "Shaw, Chad"

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    Copy number variation as a genetic basis for heterotaxy and heterotaxy-spectrum congenital heart defects
    (Royal Society, 2016-12-19) Cowan, Jason R.; Tariq, Muhammad; Shaw, Chad; Rao, Mitchell; Belmont, John W.; Lalani, Seema R.; Smolarek, Teresa A.; Ware, Stephanie M.; Pediatrics, School of Medicine
    Genomic disorders and rare copy number abnormalities are identified in 15–25% of patients with syndromic conditions, but their prevalence in individuals with isolated birth defects is less clear. A spectrum of congenital heart defects (CHDs) is seen in heterotaxy, a highly heritable and genetically heterogeneous multiple congenital anomaly syndrome resulting from failure to properly establish left–right (L-R) organ asymmetry during early embryonic development. To identify novel genetic causes of heterotaxy, we analysed copy number variants (CNVs) in 225 patients with heterotaxy and heterotaxy-spectrum CHDs using array-based genotyping methods. Clinically relevant CNVs were identified in approximately 20% of patients and encompassed both known and putative heterotaxy genes. Patients were carefully phenotyped, revealing a significant association of abdominal situs inversus with pathogenic or likely pathogenic CNVs, while d-transposition of the great arteries was more frequently associated with common CNVs. Identified cytogenetic abnormalities ranged from large unbalanced translocations to smaller, kilobase-scale CNVs, including a rare, single exon deletion in ZIC3, a gene known to cause X-linked heterotaxy. Morpholino loss-of-function experiments in Xenopus support a role for one of these novel candidates, the platelet isoform of phosphofructokinase-1 (PFKP) in heterotaxy. Collectively, our results confirm a high CNV yield for array-based testing in patients with heterotaxy, and support use of CNV analysis for identification of novel biological processes relevant to human laterality., This article is part of the themed issue ‘Provocative questions in left–right asymmetry’.
  • Thumbnail Image
    Item
    Reliable detection of subchromosomal deletions and duplications using cell-based noninvasive prenatal testing
    (Wiley, 2018-10-25) Vossaert, Liesbeth; Wang, Qun; Salman, Roseen; Zhuo, Xinming; Qu, Chunjing; Henke, David; Seubert, Ron; Chow, Jennifer; U'ren, Lance; Enright, Brennan; Stilwell, Jackie; Kaldjian, Eric; Yang, Yaping; Shaw, Chad; Levy, Brynn; Wapner, Ronald; Breman, Amy; Veyver, Ignatia Van den; Beaudet, Arthur; Medical and Molecular Genetics, School of Medicine
    Objective To gather additional data on the ability to detect subchromosomal abnormalities of various sizes in single fetal cells isolated from maternal blood, using low-coverage shotgun next-generation sequencing for cell-based noninvasive prenatal testing (NIPT). Method Fetal trophoblasts were recovered from approximately 30 mL of maternal blood using maternal white blood cell depletion, density-based cell separation, immunofluorescence staining, and high-resolution scanning. These trophoblastic cells were picked as single cells and underwent whole genome amplification for subsequent genome-wide copy number analysis and genotyping to confirm the fetal origin of the cells. Results Applying our fetal cell isolation method to a series of 125 maternal blood samples, we detected on average 4.17 putative fetal cells/sample. The series included 15 cases with clinically diagnosed fetal aneuploidies and five cases with subchromosomal abnormalities. This method was capable of detecting findings that were 1 to 2 Mb in size, and all were concordant with the microarray or karyotype data obtained on a fetal sample. A minority of fetal cells showed evidence of genome degradation likely related to apoptosis. Conclusion We demonstrate that this cell-based NIPT method has the capacity to reliably diagnose fetal chromosomal abnormalities down to 1 to 2 Mb in size.
  • Thumbnail Image
    Item
    The impact of clinical genome sequencing in a global population with suspected rare genetic disease
    (Elsevier, 2024) Thorpe, Erin; Williams, Taylor; Shaw, Chad; Chekalin, Evgenii; Ortega, Julia; Robinson, Keisha; Button, Jason; Jones, Marilyn C.; Del Campo, Miguel; Basel, Donald; McCarrier, Julie; Davis Keppen, Laura; Royer, Erin; Foster-Bonds, Romina; Duenas-Roque, Milagros M.; Urraca, Nora; Bosfield, Kerri; Brown, Chester W.; Lydigsen, Holly; Mroczkowski, Henry J.; Ward, Jewell; Sirchia, Fabio; Giorgio, Elisa; Vaux, Keith; Peña Salguero, Hildegard; Lumaka, Aimé; Mubungu, Gerrye; Makay, Prince; Ngole, Mamy; Tshilobo Lukusa, Prosper; Vanderver, Adeline; Muirhead, Kayla; Sherbini, Omar; Lah, Melissa D.; Anderson, Katelynn; Bazalar-Montoya, Jeny; Rodriguez, Richard S.; Cornejo-Olivas, Mario; Milla-Neyra, Karina; Shinaw, Marwan; Magoulas, Pilar; Henry, Duncan; Gibson, Kate; Wiaf, Samuel; Jayakar, Parul; Salyakina, Daria; Masser-Frye, Diane; Serize, Arturo; Perez, Jorge E.; Taylor, Alan; Shenbagam, Shruti; Tayoun, Ahmad Abou; Malhotra, Alka; Bennett, Maren; Rajan, Vani; Avecilla, James; Warren, Andrew; Arseneault, Max; Kalista, Tasha; Crawford, Ali; Ajay, Subramanian S.; Perry, Denise L.; Belmont, John; Taft, Ryan J.; Medicine, School of Medicine
    There is mounting evidence of the value of clinical genome sequencing (cGS) in individuals with suspected rare genetic disease (RGD), but cGS performance and impact on clinical care in a diverse population drawn from both high-income countries (HICs) and low- and middle-income countries (LMICs) has not been investigated. The iHope program, a philanthropic cGS initiative, established a network of 24 clinical sites in eight countries through which it provided cGS to individuals with signs or symptoms of an RGD and constrained access to molecular testing. A total of 1,004 individuals (median age, 6.5 years; 53.5% male) with diverse ancestral backgrounds (51.8% non-majority European) were assessed from June 2016 to September 2021. The diagnostic yield of cGS was 41.4% (416/1,004), with individuals from LMIC sites 1.7 times more likely to receive a positive test result compared to HIC sites (LMIC 56.5% [195/345] vs. HIC 33.5% [221/659], OR 2.6, 95% CI 1.9-3.4, p < 0.0001). A change in diagnostic evaluation occurred in 76.9% (514/668) of individuals. Change of management, inclusive of specialty referrals, imaging and testing, therapeutic interventions, and palliative care, was reported in 41.4% (285/694) of individuals, which increased to 69.2% (480/694) when genetic counseling and avoidance of additional testing were also included. Individuals from LMIC sites were as likely as their HIC counterparts to experience a change in diagnostic evaluation (OR 6.1, 95% CI 1.1-∞, p = 0.05) and change of management (OR 0.9, 95% CI 0.5-1.3, p = 0.49). Increased access to genomic testing may support diagnostic equity and the reduction of global health care disparities.