Rapid exome sequencing and adjunct RNA studies confirm the pathogenicity of a novel homozygous ASNS splicing variant in a critically ill neonate

Lauren S Akesson; Adam Bournazos; Andrew Fennell; Emma I Krzesinski; Kenneth Tan; Amanda Springer; Katherine Rose; Ilias Goranitis; David Francis; Crystle Lee; Fathimath Faiz; Mark R Davis; John Christodoulou; Sebastian Lunke; Zornitza Stark; Matthew F Hunter; Sandra T Cooper

doi:10.1002/humu.24101

Rapid exome sequencing and adjunct RNA studies confirm the pathogenicity of a novel homozygous ASNS splicing variant in a critically ill neonate

Hum Mutat. 2020 Nov;41(11):1884-1891. doi: 10.1002/humu.24101. Epub 2020 Sep 9.

Authors

Lauren S Akesson^{1

2

3}, Adam Bournazos^{4

5}, Andrew Fennell^{3

6}, Emma I Krzesinski^{3

6}, Kenneth Tan^{6

7}, Amanda Springer^{3

6}, Katherine Rose^{3

6}, Ilias Goranitis^{8

9}, David Francis¹, Crystle Lee¹, Fathimath Faiz¹⁰, Mark R Davis¹⁰, John Christodoulou^{1

2

9

11}, Sebastian Lunke^{1

9

12}, Zornitza Stark^{1

2

9}, Matthew F Hunter^{3

6}, Sandra T Cooper^{4

5

13}

Affiliations

¹ Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia.
² Department of Paediatrics, University of Melbourne, Melbourne, Australia.
³ Genetics Clinic, Monash Health, Monash Medical Centre, Clayton, Victoria, Australia.
⁴ Kids Neuroscience Centre, Children's Hospital at Westmead, Sydney, Australia.
⁵ Faculty of Medicine and Health, University of Sydney, Sydney, Australia.
⁶ Department of Paediatrics, Monash University, Melbourne, Australia.
⁷ Monash Newborn, Monash Health, Monash Children's Hospital, Clayton, Victoria, Australia.
⁸ Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia.
⁹ Australian Genomics Health Alliance, Parkville, Victoria, Australia.
¹⁰ Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Australia.
¹¹ Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.
¹² Department of Clinical Pathology, University of Melbourne, Melbourne, Australia.
¹³ Children's Medical Research Institute, Sydney, Australia.

PMID: 32906196
DOI: 10.1002/humu.24101

Abstract

Rapid genomic diagnosis programs are transforming rare disease diagnosis in acute pediatrics. A ventilated newborn with cerebellar hypoplasia underwent rapid exome sequencing (75 h), identifying a novel homozygous ASNS splice-site variant (NM_133436.3:c.1476+1G>A) of uncertain significance. Rapid ASNS splicing studies using blood-derived messenger RNA from the family trio confirmed a consistent pattern of abnormal splicing induced by the variant (cryptic 5' splice-site or exon 12 skipping) with absence of normal ASNS splicing in the proband. Splicing studies reported within 10 days led to reclassification of c.1476+1G>A as pathogenic at age 27 days. Intensive care was redirected toward palliation. Cost analyses for the neonate and his undiagnosed, similarly affected deceased sibling, demonstrate that early diagnosis reduced hospitalization costs by AU$100,828. We highlight the diagnostic benefits of adjunct RNA testing to confirm the pathogenicity of splicing variants identified via rapid genomic testing pipelines for precision and preventative medicine.

Keywords: ASNS; asparagine synthetase deficiency; exome sequencing; mRNA splicing analysis; rapid genomic diagnosis program.

Publication types

Case Reports
Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Aspartate-Ammonia Ligase / deficiency*
Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor / genetics*
Critical Illness
Exome Sequencing
Exons
Female
Humans
Infant, Newborn
Male
Pedigree
RNA Splice Sites
RNA Splicing*

Substances

RNA Splice Sites
Aspartate-Ammonia Ligase
Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor
ASNS protein, human