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Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract

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Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract. / Wu, Chen-Han Wilfred; Lim, Tze Y; Wang, Chunyan; Seltzsam, Steve; Zheng, Bixia; Schierbaum, Luca; Mann, Nina; Connaughton, Dervla M; Nakayama, Makiko; van der Ven, Amelie T; Dai, Rufeng; Kolvenbach, Caroline M; Kause, Franziska; Ottlewski, Isabel; Stajic, Natasa; Soliman, Neveen A; Kari, Jameela A; El Desoky, Sherif; Fathy, Hanan M; Milosevic, Danko; Turudic, Daniel; Al Saffar, Muna; Awad, Hazem S; Eid, Loai A; Ramanathan, Aravind; Senguttuvan, Prabha; Mane, Shrikant M; Lee, Richard S; Bauer, Stuart B; Lu, Weining; Hilger, Alina C; Tasic, Velibor; Shril, Shirlee; Sanna-Cherchi, Simone; Hildebrandt, Friedhelm.

In: EUR UROL OPEN SCI, Vol. 44, 09.2022, p. 106-112.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Wu, C-HW, Lim, TY, Wang, C, Seltzsam, S, Zheng, B, Schierbaum, L, Mann, N, Connaughton, DM, Nakayama, M, van der Ven, AT, Dai, R, Kolvenbach, CM, Kause, F, Ottlewski, I, Stajic, N, Soliman, NA, Kari, JA, El Desoky, S, Fathy, HM, Milosevic, D, Turudic, D, Al Saffar, M, Awad, HS, Eid, LA, Ramanathan, A, Senguttuvan, P, Mane, SM, Lee, RS, Bauer, SB, Lu, W, Hilger, AC, Tasic, V, Shril, S, Sanna-Cherchi, S & Hildebrandt, F 2022, 'Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract', EUR UROL OPEN SCI, vol. 44, pp. 106-112. https://doi.org/10.1016/j.euros.2022.08.004

APA

Wu, C-H. W., Lim, T. Y., Wang, C., Seltzsam, S., Zheng, B., Schierbaum, L., Mann, N., Connaughton, D. M., Nakayama, M., van der Ven, A. T., Dai, R., Kolvenbach, C. M., Kause, F., Ottlewski, I., Stajic, N., Soliman, N. A., Kari, J. A., El Desoky, S., Fathy, H. M., ... Hildebrandt, F. (2022). Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract. EUR UROL OPEN SCI, 44, 106-112. https://doi.org/10.1016/j.euros.2022.08.004

Vancouver

Wu C-HW, Lim TY, Wang C, Seltzsam S, Zheng B, Schierbaum L et al. Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract. EUR UROL OPEN SCI. 2022 Sep;44:106-112. https://doi.org/10.1016/j.euros.2022.08.004

Bibtex

@article{d82160c46dc44fbaa151d9e5aa1d2abe,
title = "Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract",
abstract = "BACKGROUND: Congenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of chronic kidney disease among children and adults younger than 30 yr. In our previous study, whole-exome sequencing (WES) identified a known monogenic cause of isolated or syndromic CAKUT in 13% of families with CAKUT. However, WES has limitations and detection of copy number variations (CNV) is technically challenging, and CNVs causative of CAKUT have previously been detected in up to 16% of cases.OBJECTIVE: To detect CNVs causing CAKUT in this WES cohort and increase the diagnostic yield.DESIGN SETTING AND PARTICIPANTS: We performed a genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on the same CAKUT cohort for whom WES was previously conducted.OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We evaluated and classified the CNVs using previously published predefined criteria.RESULTS AND LIMITATIONS: In a cohort of 170 CAKUT families, we detected a pathogenic CNV known to cause CAKUT in nine families (5.29%, 9/170). There were no competing variants on genome-wide CNV analysis or WES analysis. In addition, we identified novel likely pathogenic CNVs that may cause a CAKUT phenotype in three of the 170 families (1.76%).CONCLUSIONS: CNV analysis in this cohort of 170 CAKUT families previously examined via WES increased the rate of diagnosis of genetic causes of CAKUT from 13% on WES to 18% on WES + CNV analysis combined. We also identified three candidate loci that may potentially cause CAKUT.PATIENT SUMMARY: We conducted a genetics study on families with congenital anomalies of the kidney and urinary tract (CAKUT). We identified gene mutations that can explain CAKUT symptoms in 5.29% of the families, which increased the percentage of genetic causes of CAKUT to 18% from a previous study, so roughly one in five of our patients with CAKUT had a genetic cause. These analyses can help patients with CAKUT and their families in identifying a possible genetic cause.",
author = "Wu, {Chen-Han Wilfred} and Lim, {Tze Y} and Chunyan Wang and Steve Seltzsam and Bixia Zheng and Luca Schierbaum and Nina Mann and Connaughton, {Dervla M} and Makiko Nakayama and {van der Ven}, {Amelie T} and Rufeng Dai and Kolvenbach, {Caroline M} and Franziska Kause and Isabel Ottlewski and Natasa Stajic and Soliman, {Neveen A} and Kari, {Jameela A} and {El Desoky}, Sherif and Fathy, {Hanan M} and Danko Milosevic and Daniel Turudic and {Al Saffar}, Muna and Awad, {Hazem S} and Eid, {Loai A} and Aravind Ramanathan and Prabha Senguttuvan and Mane, {Shrikant M} and Lee, {Richard S} and Bauer, {Stuart B} and Weining Lu and Hilger, {Alina C} and Velibor Tasic and Shirlee Shril and Simone Sanna-Cherchi and Friedhelm Hildebrandt",
note = "{\textcopyright} 2022 The Authors.",
year = "2022",
month = sep,
doi = "10.1016/j.euros.2022.08.004",
language = "English",
volume = "44",
pages = "106--112",
journal = "EUR UROL OPEN SCI",
issn = "2666-1691",
publisher = "Elsevier BV",

}

RIS

TY - JOUR

T1 - Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract

AU - Wu, Chen-Han Wilfred

AU - Lim, Tze Y

AU - Wang, Chunyan

AU - Seltzsam, Steve

AU - Zheng, Bixia

AU - Schierbaum, Luca

AU - Mann, Nina

AU - Connaughton, Dervla M

AU - Nakayama, Makiko

AU - van der Ven, Amelie T

AU - Dai, Rufeng

AU - Kolvenbach, Caroline M

AU - Kause, Franziska

AU - Ottlewski, Isabel

AU - Stajic, Natasa

AU - Soliman, Neveen A

AU - Kari, Jameela A

AU - El Desoky, Sherif

AU - Fathy, Hanan M

AU - Milosevic, Danko

AU - Turudic, Daniel

AU - Al Saffar, Muna

AU - Awad, Hazem S

AU - Eid, Loai A

AU - Ramanathan, Aravind

AU - Senguttuvan, Prabha

AU - Mane, Shrikant M

AU - Lee, Richard S

AU - Bauer, Stuart B

AU - Lu, Weining

AU - Hilger, Alina C

AU - Tasic, Velibor

AU - Shril, Shirlee

AU - Sanna-Cherchi, Simone

AU - Hildebrandt, Friedhelm

N1 - © 2022 The Authors.

PY - 2022/9

Y1 - 2022/9

N2 - BACKGROUND: Congenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of chronic kidney disease among children and adults younger than 30 yr. In our previous study, whole-exome sequencing (WES) identified a known monogenic cause of isolated or syndromic CAKUT in 13% of families with CAKUT. However, WES has limitations and detection of copy number variations (CNV) is technically challenging, and CNVs causative of CAKUT have previously been detected in up to 16% of cases.OBJECTIVE: To detect CNVs causing CAKUT in this WES cohort and increase the diagnostic yield.DESIGN SETTING AND PARTICIPANTS: We performed a genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on the same CAKUT cohort for whom WES was previously conducted.OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We evaluated and classified the CNVs using previously published predefined criteria.RESULTS AND LIMITATIONS: In a cohort of 170 CAKUT families, we detected a pathogenic CNV known to cause CAKUT in nine families (5.29%, 9/170). There were no competing variants on genome-wide CNV analysis or WES analysis. In addition, we identified novel likely pathogenic CNVs that may cause a CAKUT phenotype in three of the 170 families (1.76%).CONCLUSIONS: CNV analysis in this cohort of 170 CAKUT families previously examined via WES increased the rate of diagnosis of genetic causes of CAKUT from 13% on WES to 18% on WES + CNV analysis combined. We also identified three candidate loci that may potentially cause CAKUT.PATIENT SUMMARY: We conducted a genetics study on families with congenital anomalies of the kidney and urinary tract (CAKUT). We identified gene mutations that can explain CAKUT symptoms in 5.29% of the families, which increased the percentage of genetic causes of CAKUT to 18% from a previous study, so roughly one in five of our patients with CAKUT had a genetic cause. These analyses can help patients with CAKUT and their families in identifying a possible genetic cause.

AB - BACKGROUND: Congenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of chronic kidney disease among children and adults younger than 30 yr. In our previous study, whole-exome sequencing (WES) identified a known monogenic cause of isolated or syndromic CAKUT in 13% of families with CAKUT. However, WES has limitations and detection of copy number variations (CNV) is technically challenging, and CNVs causative of CAKUT have previously been detected in up to 16% of cases.OBJECTIVE: To detect CNVs causing CAKUT in this WES cohort and increase the diagnostic yield.DESIGN SETTING AND PARTICIPANTS: We performed a genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on the same CAKUT cohort for whom WES was previously conducted.OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We evaluated and classified the CNVs using previously published predefined criteria.RESULTS AND LIMITATIONS: In a cohort of 170 CAKUT families, we detected a pathogenic CNV known to cause CAKUT in nine families (5.29%, 9/170). There were no competing variants on genome-wide CNV analysis or WES analysis. In addition, we identified novel likely pathogenic CNVs that may cause a CAKUT phenotype in three of the 170 families (1.76%).CONCLUSIONS: CNV analysis in this cohort of 170 CAKUT families previously examined via WES increased the rate of diagnosis of genetic causes of CAKUT from 13% on WES to 18% on WES + CNV analysis combined. We also identified three candidate loci that may potentially cause CAKUT.PATIENT SUMMARY: We conducted a genetics study on families with congenital anomalies of the kidney and urinary tract (CAKUT). We identified gene mutations that can explain CAKUT symptoms in 5.29% of the families, which increased the percentage of genetic causes of CAKUT to 18% from a previous study, so roughly one in five of our patients with CAKUT had a genetic cause. These analyses can help patients with CAKUT and their families in identifying a possible genetic cause.

U2 - 10.1016/j.euros.2022.08.004

DO - 10.1016/j.euros.2022.08.004

M3 - SCORING: Journal article

C2 - 36185583

VL - 44

SP - 106

EP - 112

JO - EUR UROL OPEN SCI

JF - EUR UROL OPEN SCI

SN - 2666-1691

ER -