RESEARCH LETTER
Exome Sequencing Reveals Compound Heterozygous Mutations in ATP8B1 in a JAG1/NOTCH2 Mutation-Negative Patient with Clinically Diagnosed Alagille Syndrome Christopher M. Grochowski,1* Ramakrishnan Rajagopalan,1 Alexandra M. Falsey,1 Kathleen M. Loomes,2,3 David A. Piccoli,2,3 Ian D. Krantz,3,4 Marcella Devoto,3,4,5,6 and Nancy B. Spinner1,7 1
Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
2
Division of Pediatric Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
3 4
Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
5
Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania Department of Molecular Medicine, University La Sapienza, Rome, Italy
6 7
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
Manuscript Received: 2 October 2014; Manuscript Accepted: 12 December 2014
TO THE EDITOR: Alagille syndrome (ALGS) is an autosomal dominant disorder characterized by bile duct paucity in combination with five primary clinical findings, including cholestasis, cardiac abnormalities (most commonly peripheral pulmonary stenosis or tetralogy of Fallot), skeletal malformations (most commonly butterfly vertebrae or other mild vertebral anomalies), ocular abnormalities (most commonly posterior embryotoxon), and characteristic facial features. Other affected systems include the kidney and vasculature, with anomalies occurring at lower frequency than in the five primary systems. Prior to the availability of genetic testing, ALGS was diagnosed clinically in individuals with bile duct paucity plus at least three of the five primary findings. The frequency of identifiable genetic mutations in ALGS patients with a clinically consistent diagnosis is high, with JAGGED1 (JAG1) mutations identified in 94% and NOTCH2 mutations in 2% of patients. We report on a female patient who presented in infancy with four out of five clinical features of ALGS, including bile duct paucity and resultant cholestasis, a cardiac murmur, posterior embryotoxon and facial features consistent with ALGS after examination by experienced clinical members of our team. These facial features included a high broad forehead, deep-set eyes and a triangular face constituting the characteristic facial features of ALGS. These findings led to a clinical diagnosis of ALGS (syndromic bile duct paucity). Echocardiography was normal by report and to our knowledge, no further cardiac workup was carried out. The patient was not reported to have butterfly vertebrae, but results of spine radiographs were not available for review. She was evaluated at our institution at age 7, at which time her main complaints were failure
Ó 2015 Wiley Periodicals, Inc.
How to Cite this Article: Grochowski CM, Rajagopalan R, Falsey AM, Loomes KM, Piccoli DA, Krantz ID, Devoto M, Spinner NB. 2015. Exome sequencing reveals compound heterozygous mutations in ATP8B1 in a JAG1/NOTCH2 mutation-negative patient with clinically diagnosed alagille syndrome. Am J Med Genet Part A 167A:891–893.
to thrive and severe pruritus refractory to multiple medications. At that time, her weight was 13.2 kg (< 3rd centile; 50th centile for 2.5 years) and height was 99.8 cm (< 3rd centile; 50th centile for 4 years). Laboratory testing done at that time revealed slightly elevated total bilirubin (1.7 mg/dl; normal range 0.6–1.4 mg/dl) and cholesterol (227 mg/dl; normal range 109–189 mg/dl). Liver enzymes were normal except for a gamma glutamyl transferase Conflict of Interest: none. Correspondence to: Christopher M. Grochowski, The Children’s Hospital of Philadelphia, Pathology and Laboratory Medicine, 3615 Civic Center Blvd Abramson Research Center Lab 1012, Philadelphia, PA 19104-4302. E-mail: [email protected] Article first published online in Wiley Online Library (wileyonlinelibrary.com): 3 March 2015 DOI 10.1002/ajmg.a.36946
891
892 (GGT) level that was slightly outside the normal range (34 U/L; normal range 13–25 U/L). Further tests revealed normal values of 25-hydroxy vitamin D, vitamin E a-tocopherol, and prothrombin time (PT). The family history included a similarly affected sibling with bile duct paucity, cardiomyopathy, posterior embryotoxon, and butterfly vertebrae, who died at 15 months of age (no biological sample was available for this individual). The proband and family members were enrolled into an IRB-approved protocol for subsequent genetic testing. Genetic analysis of the proband revealed no mutations or copy number variations in JAG1 or NOTCH2, warranting an expanded search for causal genes. We carried out exome sequencing on the proband and her parents, in order to search for other genetic changes that might explain the patient’s clinical findings. This technology permits unbiased testing and complements conventional clinical diagnoses. The exome was captured using the Agilent SureSelect V4 þ UTR target kit at a mean coverage of 100x and sequencing was carried out on an Illumina HiSeq 2500. Raw reads were aligned to the human reference genome GRCh37.69 using the Burroughs-Wheeler Aligner (BWA) tool and the Genome Analysis Toolkit (GATK) software suite was used for calling variants [Li and Durbin, 2009; Van der Auwera et al., 2013]. Variants were jointly called in the trio revealing a total of 116,554 variants. We then used SNPEFF and Gemini software suites to determine the minor allele frequencies from public databases, such as the 1000 Genomes Project [Abecasis et al., 2012] and the NHLBI Exome Sequencing Project [http://evs.gs.washington.edu/EVS/], as well as to annotate the functional consequences of the observed variants. We assumed the disease causing variants in this proband were protein altering and rare in the normal population. Out of 116,554 variants, we found 11,212 to be nonsense, frameshift, splice-site or missense variants. Filtering against dbSNP 135 to remove common variants yielded a shorter list of 337 variants. Subsequent filtering against the 1000 Genomes Phase II and ESP6500 datasets, again to remove common variants found in other populations, resulted in a final list of 129 variants for further analysis. We then tested for de novo, dominant and recessive modes of inheritance in this subset of variants and looked for genes potentially related to the phenotype in our patient. From this analysis, we identified compound heterozygous mutations in the gene ATP8B1, which is associated with two cholestatic phenotypes. These included a splice-site mutation (c.3400 þ 2 T>C) 2 bases upstream of exon 26 and a frameshift mutation (c.1889_1890insGTAAC p.His630fs) in exon 17. Sanger sequencing confirmed the mutations and parental analysis demonstrated that the splice site mutation was inherited maternally, and the frameshift was inherited paternally (Fig. 1). This is consistent with the mutations occurring in trans on the two ATP8B1 alleles in the proband (Fig. 2). Mutations in ATP8B1 are associated with both Progressive Familial Intrahepatic Cholestasis Type 1 (PFIC1), an autosomal recessive disorder that causes chronic cholestasis and eventual cirrhosis, and Benign Recurrent Intrahepatic Cholestasis (BRIC), another autosomal recessive disorder that causes cholestatic episodes without lasting damage to the liver [Bull et al., 1998]. Phenotypic presentation has been linked to mutation type, with patients bearing missense mutations more likely to have the milder BRIC phenotype, while patients with the severe clinical picture of PFIC1 are more likely to have frameshift, nonsense, and larger deletions of the gene that would significantly disrupt the function of
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
FIG. 1. Pedigree of the proband’s family showing unaffected parents, and a sibling who presented with bile duct paucity, cardiomyopathy, posterior embryotoxon, and butterfly vertebrae and died at 15 months of age (sample not available for sequencing). Sequencing of parents demonstrated the paternally inherited frameshift mutation and maternally inherited splice-site mutation.
the protein [Klomp et al., 2004]. The ATP8B1 gene encodes a P-type ATPase highly expressed in the bile canaliculi in the liver and the brush border of the intestine. ATP8B1 functions in the translocation of phospholipids between the inner and outer leaflets of the cell membrane, and plays an important role in normal bile secretion. The typical clinical presentation in PFIC1 is progressive cholestasis, pruritus, malnutrition and severe chronic diarrhea that often will not improve after liver transplantation. The liver histology in PFIC1 is characterized by canalicular cholestasis and giant cell
FIG. 2. Maternally inherited splice-site mutation, and paternally inherited frame-shift mutation shown in Sanger validation results.
GROCHOWSKI ET AL. transformation, and bile duct paucity is observed in up to 70% of cases [Alonso et al., 1994]. However, other extrahepatic features such as cardiac, ophthalmologic or skeletal manifestations are not generally observed in this patient population. Typically, levels of GGT are normal or mildly elevated in PFIC1 and highly elevated in ALGS patients. Clinical lab analysis of our patient revealed a GGT level of only 34 U/L, a surprisingly low level for individuals with Alagille Syndrome, who can present with peak values above 2,000 U/L [Emerick et al., 2008]. However, given the presence of the extrahepatic findings within our proband and a similarly affected deceased sibling, Alagille syndrome was the best clinical diagnosis prior to availability of comprehensive genetic screening technologies, such as whole exome sequencing as used here. Interestingly, a homozygous splice site mutation preceding exon 16 of the ATP8B1 gene was previously reported in multiple affected individuals within another family with atypical PFIC1. The clinical presentation was similar to that of our patient, with an initial diagnosis of Alagille syndrome and clinical features including bile duct paucity, cardiac defects and renal tubular acidosis [Copeland et al., 2013]. The finding of mutations in ATP8B1 in these two families suggests that there may be a wider spectrum of disease resulting from defects in this gene, associated with previously unrecognized extrahepatic manifestations. For this proband, having a precise diagnosis of PFIC1 (an autosomal recessive disorder) rather than ALGS (an autosomal dominant disorder) has implications for her family planning options. More broadly, this work demonstrates the power of exome sequencing to determine genetic etiology in patients lacking mutations in those genes commonly associated with their clinically diagnosed disorders. The hypothesis-free approach of wholeexome sequencing holds promise to discover the molecular bases of undiagnosed diseases with atypical presentations and therefore expand the clinical diagnostic criteria.
Online Resources Gemini: http://gemini.readthedocs.org/en/latest/ SNPEFF: http://snpeff.sourceforge.net/index.html 1000 Genomes: http://www.1000genomes.org/ Exome Sequencing Project: http://evs.gs.washington.edu/EVS/
REFERENCES Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491:56–65.
893 Alonso EM, Snover DC, Montag A, Freese DK, Whitington PF. 1994. Histologic pathology of the liver in progressive familial intrahepatic cholestasis. J Pediatr Gastroenterol Nutr 18:128–133. Bourke B, Goggin N, Walsh D, Kennedy S, Setchell KD, Drumm B. 1996. Byler-like familial cholestasis in an extended kindred. Arch Dis Child 75:223–227. Bull LN, van Eijk MJ, Pawlikowska L, DeYoung JA, Juijn JA, Liao M, Klomp LW, Lomri N, Berger R, Scharschmidt BF, Knisely AS, Houwen RH, Freimer NB. 1998. A gene encoding a P-type ATPase mutated in two forms of hereditary cholestasis. Nat Genet 18: 219–224. Cigolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Ruden SM, Lu X. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6:80–92. Copeland E, Renault N, Renault M, Dyack S, Bulman DE, Bedard K, Otley A, Fergall M, Acott P, Greer WL. 2013. Novel splice-site mutation in ATP8B1 results in atypical progressive familial intrahepatic cholestasis type 1. J Gastroenterol Hepatol 28:560–564. Emerick KM, Elias MS, Melin-Aldana H, Strautnieks S, Thompson RJ, Bull LN, Knisely AS, Whitington PF, Green RM. 2008. Bile composition in Alagille syndrome and PFIC patients having partial external biliary diversion. BMC Gastroenterol 8:47. Kaye AJ, Rand EB, Munoz PS, Spinner NB, Flake AW, Kamath BM. 2010. Effect of Kasai procedure on hepatic outcome in Alagille syndrome. J Pediatr Gastroenterol Nutr 51:319. Klomp LWJ, Vargas JC, van Mil SWC, Pawlikowska L, Strautnieks SS, van Eijk MJT, Juijn JA, Pabo´n-Pen˜a C, Smith LB, DeYoung JA, Byrne JA, Gombert J, van der Brugge G, Berger R, Jankowska I, Pawlowska J, Villa E, Knisely AS, Thompson RJ, Freimer NB, Houwen RHJ, Bull LN. 2004. Characterization of mutations in ATP8B1 associated with hereditary cholestasis. Hepatology 40: 27–38. Li H, Durbin R. 2009. Fast and accurate short read alignment with BurrowsWheeler Transform. Bioinformatics 25:1754–1760. Ling SC. 2007. Congenital cholestatic syndromes: what happens when children grow up? Can J Gastroenterol 21:743–751. Paila U, Chapman BA, Kirchner R, Quinlan AR. 2013. GEMINI: Integrative exploration of genetic variation and genome annotations. PLoS Comput Biol 9:e1003153. Summerskill WHJ. 1965. The syndrome of benign recurrent cholestasis. Am J Med 38:298–305. Van der Auwera GA, Carneiro MO, Harti C, Poplin R, del Angel G, LevyMoonshine A, Jordan T, Chakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA. 2013. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Current Protocols in Bioinformatics. 11:11.10:11.10. 1–11. 10. 33.
Exome Sequencing Reveals Compound Heterozygous Mutations in ATP8B1 in a JAG1/NOTCH2 Mutation-Negative Patient with Clinically Diagnosed Alagille Syndrome Christopher M. Grochowski,1* Ramakrishnan Rajagopalan,1 Alexandra M. Falsey,1 Kathleen M. Loomes,2,3 David A. Piccoli,2,3 Ian D. Krantz,3,4 Marcella Devoto,3,4,5,6 and Nancy B. Spinner1,7 1
Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
2
Division of Pediatric Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
3 4
Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
5
Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania Department of Molecular Medicine, University La Sapienza, Rome, Italy
6 7
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
Manuscript Received: 2 October 2014; Manuscript Accepted: 12 December 2014
TO THE EDITOR: Alagille syndrome (ALGS) is an autosomal dominant disorder characterized by bile duct paucity in combination with five primary clinical findings, including cholestasis, cardiac abnormalities (most commonly peripheral pulmonary stenosis or tetralogy of Fallot), skeletal malformations (most commonly butterfly vertebrae or other mild vertebral anomalies), ocular abnormalities (most commonly posterior embryotoxon), and characteristic facial features. Other affected systems include the kidney and vasculature, with anomalies occurring at lower frequency than in the five primary systems. Prior to the availability of genetic testing, ALGS was diagnosed clinically in individuals with bile duct paucity plus at least three of the five primary findings. The frequency of identifiable genetic mutations in ALGS patients with a clinically consistent diagnosis is high, with JAGGED1 (JAG1) mutations identified in 94% and NOTCH2 mutations in 2% of patients. We report on a female patient who presented in infancy with four out of five clinical features of ALGS, including bile duct paucity and resultant cholestasis, a cardiac murmur, posterior embryotoxon and facial features consistent with ALGS after examination by experienced clinical members of our team. These facial features included a high broad forehead, deep-set eyes and a triangular face constituting the characteristic facial features of ALGS. These findings led to a clinical diagnosis of ALGS (syndromic bile duct paucity). Echocardiography was normal by report and to our knowledge, no further cardiac workup was carried out. The patient was not reported to have butterfly vertebrae, but results of spine radiographs were not available for review. She was evaluated at our institution at age 7, at which time her main complaints were failure
Ó 2015 Wiley Periodicals, Inc.
How to Cite this Article: Grochowski CM, Rajagopalan R, Falsey AM, Loomes KM, Piccoli DA, Krantz ID, Devoto M, Spinner NB. 2015. Exome sequencing reveals compound heterozygous mutations in ATP8B1 in a JAG1/NOTCH2 mutation-negative patient with clinically diagnosed alagille syndrome. Am J Med Genet Part A 167A:891–893.
to thrive and severe pruritus refractory to multiple medications. At that time, her weight was 13.2 kg (< 3rd centile; 50th centile for 2.5 years) and height was 99.8 cm (< 3rd centile; 50th centile for 4 years). Laboratory testing done at that time revealed slightly elevated total bilirubin (1.7 mg/dl; normal range 0.6–1.4 mg/dl) and cholesterol (227 mg/dl; normal range 109–189 mg/dl). Liver enzymes were normal except for a gamma glutamyl transferase Conflict of Interest: none. Correspondence to: Christopher M. Grochowski, The Children’s Hospital of Philadelphia, Pathology and Laboratory Medicine, 3615 Civic Center Blvd Abramson Research Center Lab 1012, Philadelphia, PA 19104-4302. E-mail: [email protected] Article first published online in Wiley Online Library (wileyonlinelibrary.com): 3 March 2015 DOI 10.1002/ajmg.a.36946
891
892 (GGT) level that was slightly outside the normal range (34 U/L; normal range 13–25 U/L). Further tests revealed normal values of 25-hydroxy vitamin D, vitamin E a-tocopherol, and prothrombin time (PT). The family history included a similarly affected sibling with bile duct paucity, cardiomyopathy, posterior embryotoxon, and butterfly vertebrae, who died at 15 months of age (no biological sample was available for this individual). The proband and family members were enrolled into an IRB-approved protocol for subsequent genetic testing. Genetic analysis of the proband revealed no mutations or copy number variations in JAG1 or NOTCH2, warranting an expanded search for causal genes. We carried out exome sequencing on the proband and her parents, in order to search for other genetic changes that might explain the patient’s clinical findings. This technology permits unbiased testing and complements conventional clinical diagnoses. The exome was captured using the Agilent SureSelect V4 þ UTR target kit at a mean coverage of 100x and sequencing was carried out on an Illumina HiSeq 2500. Raw reads were aligned to the human reference genome GRCh37.69 using the Burroughs-Wheeler Aligner (BWA) tool and the Genome Analysis Toolkit (GATK) software suite was used for calling variants [Li and Durbin, 2009; Van der Auwera et al., 2013]. Variants were jointly called in the trio revealing a total of 116,554 variants. We then used SNPEFF and Gemini software suites to determine the minor allele frequencies from public databases, such as the 1000 Genomes Project [Abecasis et al., 2012] and the NHLBI Exome Sequencing Project [http://evs.gs.washington.edu/EVS/], as well as to annotate the functional consequences of the observed variants. We assumed the disease causing variants in this proband were protein altering and rare in the normal population. Out of 116,554 variants, we found 11,212 to be nonsense, frameshift, splice-site or missense variants. Filtering against dbSNP 135 to remove common variants yielded a shorter list of 337 variants. Subsequent filtering against the 1000 Genomes Phase II and ESP6500 datasets, again to remove common variants found in other populations, resulted in a final list of 129 variants for further analysis. We then tested for de novo, dominant and recessive modes of inheritance in this subset of variants and looked for genes potentially related to the phenotype in our patient. From this analysis, we identified compound heterozygous mutations in the gene ATP8B1, which is associated with two cholestatic phenotypes. These included a splice-site mutation (c.3400 þ 2 T>C) 2 bases upstream of exon 26 and a frameshift mutation (c.1889_1890insGTAAC p.His630fs) in exon 17. Sanger sequencing confirmed the mutations and parental analysis demonstrated that the splice site mutation was inherited maternally, and the frameshift was inherited paternally (Fig. 1). This is consistent with the mutations occurring in trans on the two ATP8B1 alleles in the proband (Fig. 2). Mutations in ATP8B1 are associated with both Progressive Familial Intrahepatic Cholestasis Type 1 (PFIC1), an autosomal recessive disorder that causes chronic cholestasis and eventual cirrhosis, and Benign Recurrent Intrahepatic Cholestasis (BRIC), another autosomal recessive disorder that causes cholestatic episodes without lasting damage to the liver [Bull et al., 1998]. Phenotypic presentation has been linked to mutation type, with patients bearing missense mutations more likely to have the milder BRIC phenotype, while patients with the severe clinical picture of PFIC1 are more likely to have frameshift, nonsense, and larger deletions of the gene that would significantly disrupt the function of
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
FIG. 1. Pedigree of the proband’s family showing unaffected parents, and a sibling who presented with bile duct paucity, cardiomyopathy, posterior embryotoxon, and butterfly vertebrae and died at 15 months of age (sample not available for sequencing). Sequencing of parents demonstrated the paternally inherited frameshift mutation and maternally inherited splice-site mutation.
the protein [Klomp et al., 2004]. The ATP8B1 gene encodes a P-type ATPase highly expressed in the bile canaliculi in the liver and the brush border of the intestine. ATP8B1 functions in the translocation of phospholipids between the inner and outer leaflets of the cell membrane, and plays an important role in normal bile secretion. The typical clinical presentation in PFIC1 is progressive cholestasis, pruritus, malnutrition and severe chronic diarrhea that often will not improve after liver transplantation. The liver histology in PFIC1 is characterized by canalicular cholestasis and giant cell
FIG. 2. Maternally inherited splice-site mutation, and paternally inherited frame-shift mutation shown in Sanger validation results.
GROCHOWSKI ET AL. transformation, and bile duct paucity is observed in up to 70% of cases [Alonso et al., 1994]. However, other extrahepatic features such as cardiac, ophthalmologic or skeletal manifestations are not generally observed in this patient population. Typically, levels of GGT are normal or mildly elevated in PFIC1 and highly elevated in ALGS patients. Clinical lab analysis of our patient revealed a GGT level of only 34 U/L, a surprisingly low level for individuals with Alagille Syndrome, who can present with peak values above 2,000 U/L [Emerick et al., 2008]. However, given the presence of the extrahepatic findings within our proband and a similarly affected deceased sibling, Alagille syndrome was the best clinical diagnosis prior to availability of comprehensive genetic screening technologies, such as whole exome sequencing as used here. Interestingly, a homozygous splice site mutation preceding exon 16 of the ATP8B1 gene was previously reported in multiple affected individuals within another family with atypical PFIC1. The clinical presentation was similar to that of our patient, with an initial diagnosis of Alagille syndrome and clinical features including bile duct paucity, cardiac defects and renal tubular acidosis [Copeland et al., 2013]. The finding of mutations in ATP8B1 in these two families suggests that there may be a wider spectrum of disease resulting from defects in this gene, associated with previously unrecognized extrahepatic manifestations. For this proband, having a precise diagnosis of PFIC1 (an autosomal recessive disorder) rather than ALGS (an autosomal dominant disorder) has implications for her family planning options. More broadly, this work demonstrates the power of exome sequencing to determine genetic etiology in patients lacking mutations in those genes commonly associated with their clinically diagnosed disorders. The hypothesis-free approach of wholeexome sequencing holds promise to discover the molecular bases of undiagnosed diseases with atypical presentations and therefore expand the clinical diagnostic criteria.
Online Resources Gemini: http://gemini.readthedocs.org/en/latest/ SNPEFF: http://snpeff.sourceforge.net/index.html 1000 Genomes: http://www.1000genomes.org/ Exome Sequencing Project: http://evs.gs.washington.edu/EVS/
REFERENCES Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491:56–65.
893 Alonso EM, Snover DC, Montag A, Freese DK, Whitington PF. 1994. Histologic pathology of the liver in progressive familial intrahepatic cholestasis. J Pediatr Gastroenterol Nutr 18:128–133. Bourke B, Goggin N, Walsh D, Kennedy S, Setchell KD, Drumm B. 1996. Byler-like familial cholestasis in an extended kindred. Arch Dis Child 75:223–227. Bull LN, van Eijk MJ, Pawlikowska L, DeYoung JA, Juijn JA, Liao M, Klomp LW, Lomri N, Berger R, Scharschmidt BF, Knisely AS, Houwen RH, Freimer NB. 1998. A gene encoding a P-type ATPase mutated in two forms of hereditary cholestasis. Nat Genet 18: 219–224. Cigolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Ruden SM, Lu X. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6:80–92. Copeland E, Renault N, Renault M, Dyack S, Bulman DE, Bedard K, Otley A, Fergall M, Acott P, Greer WL. 2013. Novel splice-site mutation in ATP8B1 results in atypical progressive familial intrahepatic cholestasis type 1. J Gastroenterol Hepatol 28:560–564. Emerick KM, Elias MS, Melin-Aldana H, Strautnieks S, Thompson RJ, Bull LN, Knisely AS, Whitington PF, Green RM. 2008. Bile composition in Alagille syndrome and PFIC patients having partial external biliary diversion. BMC Gastroenterol 8:47. Kaye AJ, Rand EB, Munoz PS, Spinner NB, Flake AW, Kamath BM. 2010. Effect of Kasai procedure on hepatic outcome in Alagille syndrome. J Pediatr Gastroenterol Nutr 51:319. Klomp LWJ, Vargas JC, van Mil SWC, Pawlikowska L, Strautnieks SS, van Eijk MJT, Juijn JA, Pabo´n-Pen˜a C, Smith LB, DeYoung JA, Byrne JA, Gombert J, van der Brugge G, Berger R, Jankowska I, Pawlowska J, Villa E, Knisely AS, Thompson RJ, Freimer NB, Houwen RHJ, Bull LN. 2004. Characterization of mutations in ATP8B1 associated with hereditary cholestasis. Hepatology 40: 27–38. Li H, Durbin R. 2009. Fast and accurate short read alignment with BurrowsWheeler Transform. Bioinformatics 25:1754–1760. Ling SC. 2007. Congenital cholestatic syndromes: what happens when children grow up? Can J Gastroenterol 21:743–751. Paila U, Chapman BA, Kirchner R, Quinlan AR. 2013. GEMINI: Integrative exploration of genetic variation and genome annotations. PLoS Comput Biol 9:e1003153. Summerskill WHJ. 1965. The syndrome of benign recurrent cholestasis. Am J Med 38:298–305. Van der Auwera GA, Carneiro MO, Harti C, Poplin R, del Angel G, LevyMoonshine A, Jordan T, Chakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA. 2013. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Current Protocols in Bioinformatics. 11:11.10:11.10. 1–11. 10. 33.
