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Environmental bacteria from Hong Kong seawater

ABSTRACT: Environmental bacteria from Hong Kong seawater Raw sequence reads

PROVIDER: PRJNA817672 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR18428471_1.fastq.gz	Fastqsanger.gz
	SRR18428471_2.fastq.gz	Fastqsanger.gz
	SRR18428472_1.fastq.gz	Fastqsanger.gz
	SRR18428472_2.fastq.gz	Fastqsanger.gz
	SRR18428473_1.fastq.gz	Fastqsanger.gz

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Project description:The project aim is to evaluate the role of whole-genome aCGH for prenatal diagnosis in Hong Kong. Array CGH was performed on 220 samples recruited prospectively as the first-tier test study; and on 150 samples with abnormal ultrasound findings and normal karyotypes as a further-test study using NimbleGen CGX-135K oligonucleotide arrays. After the exclusion of common aneuploidies in the first-tier study, clinically significant CNVs are detected in 23/220 samples. In the further test study, clinically significant CNVs are detected in 9/150 samples, which showed CGX array has an increased diagnostic yield of about 6% compared with conventional cytogenetic methods. CNVs of unclear clinical significance are detected in only 10/370 (2.7%) samples. Only data from sample with positive findings are included in this experiment submission (the samples with normal results are not included here).

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Project description:Objective: To evaluate the clinical impact of chromosomal microarray (CMA) on the management of paediatric patients in Hong Kong Methods: We performed NimbleGen 135k oligonucleotide array on 327 children with intellectual disability (ID)/ developmental delay (DD), autism spectrum disorders (ASD), and/or multiple congenital anomalies (MCAs) in a university-affiliated paediatric unit from January 2011 to May 2013. The medical records of patients were reviewed in September 2013, focusing on the pathogenic/likely pathogenic CMA findings and their “clinical actionability” based on established criteria. Results: Thirty-seven patients were reported to have pathogenic/likely pathogenic results, while 40 had findings of unknown significance. This gives a detection rate of 11% for clinically significant (pathogenic/likely pathogenic) findings. The significant findings have prompted clinical actions in 28 out of 37 patients (75.7%), while the findings with unknown significance have led to further management recommendation in only 1 patient (p<0.001). Nineteen out of the 28 management recommendations are “evidence-based” on either practice guidelines endorsed by a professional society (n=9, Level 1) or peer-reviewed publications making medical management recommendation (n=10, Level 2). CMA results impact medical management by precipitating referral to a specialist (n=24); diagnostic testing (n=24), surveillance of complications (n=19), interventional procedure (n=7), medication (n=15) or lifestyle modification (n=12).

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