article: Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that results in progressive degeneration of motor neurons, ultimately leading to paralysis and death. Approximately 10% of ALS cases are familial, with the remaining 90% of cases being sporadic. Genetic studies in familial cases of ALS have been extremely informative in determining the causative mutations behind ALS, especially as the same mutations identified in familial ALS can also cause sporadic disease. However, the cause of ALS in approximately 30% of familial cases and in the majority of sporadic cases remains unknown. Sporadic ALS cases represent an underutilized resource for genetic information about ALS; therefore, we undertook a targeted sequencing approach of 169 known and candidate ALS disease genes in 242 sporadic ALS cases and 129 matched controls to try to identify novel variants linked to ALS. We found a significant enrichment in novel and rare variants in cases versus controls, indicating that we are likely identifying disease associated mutations. This study highlights the utility of next generation sequencing techniques combined with functional studies and rare variant analysis tools to provide insight into the genetic etiology of a heterogeneous sporadic disease.
  Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that primarily affects motor neurons, resulting in progressive paralysis and death [1]. About 2 in 100,000 people per year are diagnosed with ALS and the disease is often ruthlessly progressive, with death occurring between 2–5 years after disease onset. Currently, there is only one treatment for ALS, riluzole, which extends lifespan by approximately three months. The majority of ALS cases are sporadic, meaning that they occur with no family history of the disease (sALS). The remaining 5–10% of cases are familial (fALS), where the disease is inherited in a Mendelian, generally dominant, fashion within a family. While sALS has a complex etiology, with both environmental and genetic factors thought to play a role, in recent years several genes have been linked to both fALS and sALS. Previous studies to identify causative genes in ALS have primarily been carried out in families and some genes identified in fALS studies have subsequently been found to be mutated in sALS cases as well (e. g. , [2]–[4]). Indeed, in the past few years there has been an explosion in the number of genes linked to ALS, in part due to the accessibility of next generation sequencing techniques [1]. However, as the number of large uncharacterized fALS pedigrees decreases, new approaches will be needed to expand the genetic landscape of ALS. One can imagine several approaches to this problem. First, candidate approaches can be carried out, based on what is currently known about the biology of ALS. For example, we previously used a candidate approach to identify novel ALS disease genes by looking for genes that behaved similarly to the well-known ALS disease genes, TARDBP and FUS. Both TDP-43 (the protein product of the TARDBP gene) and FUS contain RNA Recognition Motifs (RRMs) and prion-like domains, and aggregate and are toxic in yeast, mimicking their behavior in disease [5], [6]. Using these characteristics, we looked for other RRM-containing proteins that also aggregated and were toxic in yeast; of the 133 proteins we tested, 38 aggregated and were toxic in yeast [7]. Out of these we were particularly interested in two genes, TAF15 and EWSR1; first because they also contain prion-like domains and second because they are in the same gene family as FUS [7], [8]. Subsequent Sanger sequencing of EWSR1 and TAF15 in sALS cases led to the identification of variants that were present in ALS cases but not in controls [7], [8]. Since then some of the other candidate genes from this yeast screen were independently linked to ALS or related neuromuscular disorders. For example, mutations in hnRNPA1 and hnRNPA2/B1 were found in ALS families and in multisystem proteinopathy [9], TIA1 mutations were identified in Welander distal myopathy [10], [11] and also associated with stress granule formation in ALS [12]. Finally a mutation in hnRPDL was found to cause limb-girdle muscular dystrophy 1G [13]. Another approach is to take advantage of small families. Variants in ErbB4 were recently associated with ALS using small pedigrees and sporadic cases [14]. We used a similar approach to identify new candidate disease genes by studying trios – families with an affected proband and two unaffected parents – to ask if we could uncover de novo mutations that are present in the affected proband, but not in the unaffected parents. This approach allowed us to identify approximately 25 new candidate ALS disease genes, including SS18L1/CREST, which is a member of the nBAF complex and is required for proper neurite outgrowth [15]. Finally, one could also imagine taking advantage of the large number of sALS patient samples, as has been done with the many genome wide association studies (GWAS) previously performed for ALS [16], [17]. While studies performed solely with sALS cases lack the Mendelian power that familial studies have, these studies make up for this deficiency with numbers – there are large numbers of sporadic ALS samples available for study. Unfortunately GWASs are often inconclusive and sometimes the results cannot be replicated [16]–[18]. For ALS, several independent GWASs pinpointed the chromosome 9p21 region as associated with ALS [17]–[20]. As the numbers of cases and controls analyzed by GWAS increases, additional loci are being implicated and warrant further investigation and validation [18], [21]. However, evidence from twin and other studies strongly suggest that there is a heritability component to sALS and thus genetic approaches, such as whole genome or more targeted sequencing methods, should be useful in identifying causative variants in sALS [18], [22]–[24]. Additionally, de novo mutations in genes like SOD1 and FUS have been identified in sporadic cases of ALS [25]–[27]. The main challenge of studying sALS is that the variants responsible for ALS are likely not shared between individuals and may not even be in the same gene. The challenge of statistically evaluating rare variants in biologically relevant genes has been addressed by rare variant binning methods [28], [29]. As such, we decided to take advantage of the proliferation and reduction in cost of next generation sequencing techniques to test this idea in the untapped resource of sALS samples. Because GWAS does not pick up the disease relevant rare and novel variation and full exome or genome sequencing analysis would focus on candidate genes anyway, we targeted a large set of candidate disease genes in a cohort of sALS patients and controls [30]. This allowed us to test several hypotheses: (1) can we find new variants in known ALS disease genes? (2) can we find new variants in genes implicated by GWAS and other studies and test previously identified variants in our cohort? (3) can we find new variants or confirm previously identified ones in the set of candidate genes generated from our previous ALS trios study [15]? And (4) can we identify an enrichment in variants in genes containing RNA recognition motifs (RRMs), like TDP-43 and FUS [7], [8]? We sequenced all exons of 169 genes in 242 ALS patients and 129 age-matched controls from the Coriell Cell Repository (http: //ccr. coriell. org/). While no one gene was significantly enriched between cases and controls, we saw an enrichment of deleterious rare and novel variation across previously implicated ALS genes between cases and controls. Additionally, we identified new variants in known ALS disease genes, as well as in genes associated with ALS, found no association between several previously identified SNPs and ALS in our population, with the exception of APOE, and identified new variants in genes identified through our trio and RRM studies [7], [8], [15]. This study demonstrates the utility of hypothesis-driven targeted sequencing for identifying disease-relevant novel and rare variation, as we did observe an increase in novel and rare variants in our cases versus controls, but also highlights the challenges and limitations of such studies and the need for further studies with more patient and control samples. Moreover, we also present the application of rare variant binning to show that sALS individuals have a higher burden of deleterious mutations in previously implicated ALS genes.
  We sequenced 169 candidate genes in 242 patients and 129 age-matched controls using the HaloPlex technology with a custom designed library (Agilent; Table S1). This method results in the exon capture of a specific customized library of genes allowing for the rapid screening of a limited number of genes across many samples. We initially attempted to sequence 276 patients and 184 controls, but the HaloPlex enrichment did not work for all samples. For the samples that were included, on average, 50,000,000 reads with a mean coverage of 55 reads per base and 65% of the bases having more than 10 reads was generated for each sample. The pre-determined candidate genes sequenced in this study fell into four categories (Figure 1A; Table S1): genes with prior evidence to affect ALS (Known ALS), genes that were potentially associated with ALS through GWAS (Associated), candidate genes from our previously published analysis of ALS trios (Trios) [15] and genes containing RNA Recognition Motifs (RRM) that also had high prion scores or were very toxic in our previously published yeast screen [31]. Some genes fell into multiple categories; for example, FUS is categorized as a known ALS gene, however, it also contains an RRM and prion domain. In total, we found 134 novel variants (not present in ESP6500,1000genomes, or dbSNPv137) in ALS patients versus 61 novel variants in controls (Tables S2, S3). One variant was found in two ALS patients and in one control and was removed from further analysis, as its presence in both populations suggests that it is likely a benign polymorphism. Given that rare variants can also contribute to disease [32], we asked how many rare variants were present in our samples (variants that were already present in either ESP6500,1000genomes or dbSNPv137 but at very low frequencies). We chose a frequency of equal to or less than 0. 000538 in the ESP6500 database (http: //evs. gs. washington. edu/EVS/) as our cut off point, since this is the frequency of one of the known, disease causing, SOD1 mutations present in our dataset (p. D91A, rs80265967, [33]). Variants found in both cases and controls were removed, resulting in the identification of 99 rare variants in ALS cases and 41 in controls (Tables S4 and S5). We then asked how many of our case and control samples harbored novel or rare variants. Of the 242 patients sequenced, we found rare or novel variants in 144 of these, suggesting that at minimum approximately 40% of the cases have no potential genetic cause for ALS that we could identify with our sequencing method and set of candidate genes. We did not expect to be able to explain all ALS cases, as genes outside this library are also likely to be responsible for ALS, noncoding regions are also potentially involved (e. g. regulatory regions or C9ORF72-like intronic expansions [20]), and environmental factors are also known to play a role in the etiology of ALS [1]. Of the 129 control samples that were sequenced, novel or rare variants were found in 69 samples (47% without). While no single gene emerged as significantly enriched in our analysis, we did find several genes that trended towards more novel and rare variants in ALS patient samples versus controls (Figure 1B and Table S1), including SRCAP (trios, 10 novel or rare variants in patients versus 2 in controls) and AIM1L (trios, 5 novel or rare variants in patients versus 1 in controls). These, and other individual genes, are discussed in more detail below. There are 22 genes that we considered to be ALS disease causing genes (Table S1) and we tested whether we could uncover either known disease causing variants or novel variants in our cohort. Genes that were listed in OMIM (http: //www. ncbi. nlm. nih. gov/omim) as causing or increasing susceptibility to ALS were included in this list, as well as two genes that have very recently been tied to sporadic ALS and frontotemporal lobar degeneration (FTLD), EWSR1 and TAF15 [7], [8], [34]. This patient set from Coriell has been prescreened for TARDBP mutations, and we confirmed that none of the patients carried mutations in this gene. As is perhaps to be expected, we uncovered known ALS causing mutations in SOD1 in three of our patient samples (Table S4 and S6, Figure 1C); however, these were the only known ALS causing mutations that we uncovered. In addition to these known variants, we found 22 novel variants in known ALS disease genes in cases and 8 novel variants in controls (Table S7). Of particular interest was that several of these novel variants are located very close to known ALS-linked variants, suggesting that they may indeed be causative. For example, we found novel variants in ANG, ALS2, ATXN2, FUS, SETX, SOD1, and TAF15 (for full list, see Table S7). While only about 20 genes have been conclusively linked to ALS, many more have been studied in connection to ALS. For example, as of November 2013, there are 17 studies returned in a search for ALS GWAS in the catalog of published genome-wide association studies maintained by the National Human Genome Research Institute (http: //www. genome. gov/gwastudies). In these studies, approximately 70 regions were associated with ALS over the control populations. While some of these emerged in several studies (e. g. the region containing C9ORF72), many only appear once [18]. Several SNPs have also been linked to ALS through other means, including candidate gene approaches (e. g. [54]). Currently, many genes linked to ALS are of unknown significance in the disease, as studies often report conflicting results (e. g. [54] vs. [55]). We therefore asked of approximately 80 of these genes (associated) if we could find new variants or confirm previously identified ones in our patient population (Table S1, S2). We looked for enrichment of deleterious rare or novel alleles in known and associated genes using a modified version of a previously described method for allele binning [28]. We focused on known and associated genes because these genes have a high prior for involvement in ALS, and this method has been previously shown to work specifically using genes with prior biological evidence. This method incorporates Polyphen-2 scores and thus downweights any variation that is not predicted to be deleterious to the protein. Using this method, we found a significant difference in the distribution of deleterious variation between cases and controls (Fisher' s Exact test, p = 0. 019, OR = 1. 93,95% CI: 1. 11–3. 51, Table S8). We previously attempted to identify new ALS disease genes in sALS cases by studying trios, which are made up of two unaffected parents and an affected proband – the idea being that the proband will have a de novo mutation that is not present in either parent [15]. This approach has previously been used to great effect to study the genetics of autism, intellectual disability, and schizophrenia [111]–[117] and when applied to ALS trios revealed several de novo, novel variants [15]. We therefore asked if we could identify further variants in these ALS candidate genes from the trio analysis in a larger data set, so we sequenced several of these genes as part of our HaloPlex analysis. One of the variants identified in the ALS trios study was a nonsense mutation that removed the last nine amino acids of a protein called SS18L1/CREST. SS18L1 is a member of the nBAF complex and is thus involved in chromatin remodeling and it has also been implicated in neurite outgrowth [15], [118]–[121]. Additionally, a second novel missense mutation was found in one member of a family with ALS, p. I123M [15]. More recently two new SS18L1 variants were identified in a cohort of 87 fALS patients: one novel missense mutation, p. A264T, and one deletion, p. G222_S224del [122]. In this new patient cohort we found a novel variant in SS18L1 at p. G168V and a rare variant at p. G151S; no novel or rare variants were found in the control samples (Tables S2–S5). In addition to SS18L1, several other genes involved in chromatin regulation were also enriched in the dataset, including EHMT1, FOXA1, HDAC10, and SRCAP, which was one of the genes with the most rare or novel variants in our HaloPlex dataset (Table S2) [15]. We identified 10 novel or rare variants in SRCAP in patients versus only 2 in controls (Tables S1–S5, Figure 2). SRCAP has a very low RVIS (Residual Variance Intolerence Score) at −4. 14 (Table S1). RVIS scores are a measure of genic intolerance to functional variation and low RVIS scores have been shown to be a good predictor of whether or not a variant is likely to be disease causing, as a gene with very high genic intolerance (a low RVIS score) would be less likely to tolerate random variation, and thus variations within that gene are more likely to be deleterious [123]. However, it is worth noting that SOD1, in which virtually any mutation will lead to ALS, has a relatively high RVIS score of −0. 08. A de novo frameshift was also identified in SRCAP in the trio study, which results in truncation of the protein, similar to SSI8L1 [15]. Also similar to SS18L1, SRCAP is a CBP-interacting transcriptional co-activator [124]. Heterozygous mutations in SRCAP have been extensively linked to Floating-Harbor syndrome, which is characterized by low birth weight, short stature, skeletal anomalies, and intellectual disability [125]. If SRCAP is indeed an ALS disease gene, this further underscores the potential link between neurodevelopmental and neurodegenerative diseases [15]. As for the other three chromatin remodeling genes that came out of the trio study, we found 5 novel and rare variants in EHTM1, and 1 novel variant each in FOXA1 and HDAC10 (Table S1–S5) [15]. The central role that RNA binding proteins play in ALS has been emerging over the past few years, as more and more RNA binding proteins surface as ALS disease genes [1], [126], [127]. This list includes ANG, ATXN2, FUS, TARDPB, TAF15, EWSR1, SETX, and more recently hnRNPA2/B1 and hnRNPA1 [1], [9]. Several of these genes contain both RNA Recognition Motif domains (RRM), a small ∼80 amino acids domain that binds single-stranded RNA [128], and a prion-like domain [7], [126], [127]. We wondered whether there might be an increased load of rare or novel variants in other proteins that had RRM and prion-like domains in ALS cases. In this experiment, we sequenced 30 RRM genes with the highest prion domain scores or the highest toxicity scores that were identified in our previously published yeast assay [7], [8]. While we did not find any enrichment in variants in this gene set, we did find a number of rare and novel variants in these genes, suggesting that sequencing a larger set of genes in a bigger sample set in the future would be beneficial (Table S2, S4). In addition to the rare and novel variants in TAF15 and EWSR1 discussed above, we also found 17 novel and rare variants in genes including RBM33, CELF4, and SFPQ (Table S1, S2, S4). Further specific examples are discussed below.
  We used a candidate gene approach to discover new mutations in biologically relevant ALS genes using sporadic ALS cases. Additionally, we used a large array of tools to study newly identified variants and assess relevance to disease. We used functional studies, when possible, to compare newly identified variants with other ALS variants. We also used bioinformatics tools to assess variant pathogenicity and combined it with a rare variant binning approach to demonstrate that cases have a higher burden of deleterious mutations than controls. This supports the idea that novel or rare mutations in a set of key genes may contribute to sporadic ALS. The abundance and relative affordability of next generation sequencing techniques has launched a new era in the study of human disease. Suddenly, the capacity to discover the causative mutation behind disease seems almost at one' s fingertips. This approach is more straightforward in homogenous diseases, or in cases where large families are available. However, for a heterogeneous disease like ALS, where the majority of the cases are sporadic, more creative approaches are required. We took advantage of the HaloPlex target capture system (Agilent) to rapidly sequence a set of 169 candidate genes in 242 patients and 129 controls to ask if we could (1) identify new mutations in known ALS disease genes, (2) find further evidence that genes previously associated with ALS are indeed causative, (3) find new mutations in candidates generated from our previously performed study with ALS trios and finally, (4) ask if we could find variants in RNA binding proteins. This candidate gene approach has both benefits and drawbacks. By focusing on a list of genes, those genes could be sequenced more rapidly and cost effectively than whole exome or genome sequencing. However, there is an inherent bias in this method since we are only testing the genes we chose to sequence, and could very well be missing important variants in genes outside of our gene set. Thus, even when using a whole exome or genome sequencing approach with a limited number of patients, the first pass analysis focuses on biologically relevant candidate genes. Therefore, a candidate gene based panel may be a more cost effective way of assessing sporadic disease in a particular population. For example, many neuromuscular diseases have similar clinical manifestations, and can be challenging to diagnose precisely in their early stages. A panel of ∼500 known causative genes can easily be created as a" neuromuscular diagnostic kit" and be sequenced looking for known or novel variants. This approach would be faster and cheaper than the current practice of iteratively performing dozens of traditional Sanger sequencing tests and would considerably help to streamline clinical diagnostic processes. Alternatively, this technique could be used as it was in this study, to quickly probe a large set of potential disease genes, for which there is not conclusive evidence of their linkage to a disease. Using the novel approach of sequencing many candidate genes in many patients and controls using the HaloPlex method has yielded a plethora of genetic information. Viewed as a whole, we found a statistically significant enrichment of deleterious novel and rare variants in patients versus controls, suggesting that deleterious variation across a set of biologically relevant genes may be responsible for sporadic ALS. Our method, which combined polyphen-2 scores and binned variation, combined with functional studies and additional bioinformatics approaches allowed us to have statistical power to identify a difference between two groups. A common problem for assessing rare variation is the lack of statistical power – here we demonstrated an example of an allele binning strategy as a means of showing the importance of a biologically relevant set of genes. When we looked closer at our dataset, we found several interesting variants in each of the four categories of genes that we tested (known ALS genes, genes associated with ALS, genes from a previous trio analysis and genes with RRM). For example, we provide further evidence that point mutations ALS2 and SETX may cause adult onset ALS in addition to their tradition role as juvenile ALS disease genes [35], [39]–[42], [44]. We found a novel variant in FUS (Y526C), which in a functional study caused mislocalization of the protein from the nucleus to the cytoplasm, similar to other disease-causing FUS variants (Figure 2). When we analyzed genes associated with ALS, we found that in our patient population the ε2 allele of APOE is associated with limb onset ALS, while the ε4 allele is associated with an earlier age of onset in limb onset ALS, and is also more frequent in female limb onset ALS patients. When we sequenced the genes uncovered in our previously published trio analysis [15], we found many novel and rare variants in SRCAP, suggesting that it merits further study as a potential ALS disease gene. Finally, we identified many novel and rare variants in genes containing RRM motifs, including in hnRNPA1 and hnRNPA2/B1, which have both been recently linked to ALS [9]. In this report, we have analyzed only nonsynonymous variants, as those are the changes that we best understand the consequences of. However, a huge portion of the variants that we identified result in synonymous changes; thus there is a large untapped part of our dataset that may turn out to be relevant to disease. This will be an area for future exploration and data analysis, as our understanding of the effects of synonymous variation grows. But even for nonsynonymous changes, assessing pathogenicity for a given variant can be very challenging. For known genes, were their role in ALS is already fairly well characterized (e. g. , SOD1 and FUS) it is reasonable to design functional studies to verify that newly identified variants behave similarly to the ones previously linked with ALS. This is the approach we took to assess pathogenicity of the novel Y526C FUS variant (Figure 2). Since this variant is located within a conserved NLS and nearby other pathogenic mutations (e. g. , P525L), we were able to test the effect on FUS nuclear localization and demonstrated that the mutation caused redistribution to the cytoplasm (Figure 2), in support of the pathogenicity of the variant. For other candidate genes from our study, like SPG11, SRCAP, AIM1L, it is less feasible to design studies to assess the impact of variants of different classes for function, when much less is known about the normal functions of these genes. Some of these candidate genes are involved in other diseases, like SPG11 for example, which is also involved in Hereditary Spastic Paraplegia [109]. Are the functional studies used to test for these diseases relevant to ALS? SRCAP, which encodes a chromatin-remodeling factor [140], implicates potential effects on chromatin remodeling. However, are alterations in the chromatin-remodeling activity of SRCAP responsible for ALS, or is it another still unknown function? Finally, for genes like AIM1L (absent in melanoma 1-like), where almost nothing is known about the function of the gene product, designing informative functional studies to assess the effect of variants is not feasible. Even if a variant does functionally impact the protein it still may not be pathogenic. These issues make it a challenge to distinguish true disease-causing variants from benign ones. Clearly, new rigorous approaches will be required to help make the results of sequencing studies like this one clinically informative [141]. Familial ALS appears to be a much more homogenous disease than sporadic ALS, as approximately 20 known genes can explain about 60% of cases [1]. However, much fewer than 60% of sporadic cases have a definitive genetic cause, with mutations in known disease causing genes appearing at much lower frequencies than in fALS [1]. For example, one study found that expansions in C9ORF72 were present in ∼40% of fALS cases, but only in ∼7% of sALS cases [142]. This suggests that the genetic causes of sporadic ALS are likely to be many and varied, that the well known ALS disease genes can only explain so much, and that broad techniques will be necessary to identify causative mutations in sALS. It is the hope as well that, just as mutations in genes discovered in fALS have been informative for sALS, the reverse will be true. Additionally, as the lines continue to blur between various neurodegenerative diseases, causative mutations found in sALS may also be relevant to other neurodegenerative diseases, such as frontotemporal dementia, Alzheimer' s disease, and Parkinson' s disease. As a proof of principle study, we believe that our results prove the utility of combining sporadic ALS samples with the power of next generation sequencing techniques and that future studies will yield useful genetic information for the study of ALS in general. By taking advantage of this untapped resource, there is a whole new set of samples available for study. An oligogenic hypothesis in which sporadic ALS appears and disappears randomly as the multiple mutations necessary for disease arise in some individuals due to the random shuffling of alleles from one generation to the next is emerging, and will perhaps be best studied using next generation sequencing techniques [47]. We believe that future studies using next generation sequencing techniques on large numbers of sALS patient samples will be fruitful for further understanding the genetics of ALS. As our knowledge of ALS grows, it seems more to be a field of icebergs connected under the surface, rather than just one, underscoring the importance of continued genetic studies of ALS.
  We sequenced three ALS panels and two control panels from the Coriell collection of North American Caucasian DNA samples (http: //www. ccr. coriell. org). NDPT025 contained samples from ALS patients that survived for 7 years or longer, NDPT026 contained patient samples from ALS patients with bulbar onset, and NDPT103 contained patient samples from ALS patients with upper-limb onset. Only patients without a family history of ALS were included in these panels and all patients met the EI Escorial criteria for definite, probable or possible ALS. Of the 242 patient samples that we sequenced, 111 were females and 131 were male and the age of onset ranged from 44 to 82 years of age, with an average age of onset of 60. More detailed information about each patient is publicly available and can be found through Coriell by searching for the plate or sample number provided on Coriell website. We sequenced 129 samples from two panels of age-matched controls, NDPT084 and NDPT099, with age at sampling from 55–88 and no family history of neurological disease, of which 69 samples were from women and 60 from men. Using the Agilent SureDesign online tool (https: //earray. chem. agilent. com/suredesign/), a HaloPlex custom kit (Agilent, Santa Clara, CA, https: //www. agilent. com) was designed to include all exons of target genes previously linked with ALS and listed in ALSoD [143] (http: //alsod. iop. kcl. ac. uk/) (associated and known ALS categories), candidates genes from our previous study using ALS Trios [15] (trio category), and finally RRM genes harboring a high prion score domain or with a high toxicity score [7], [8] (RRM category) (Table S1). Five indexed paired-end Illumina sequencing libraries [144] were generated according to the HaloPlex HaloPlex manufacturer' s protocol, one DNA library per 96-well plate. Sequencing was performed with 150 bp paired-end reads on an Illumina MiSeq machine. About 30% of the SNPs were Sanger sequenced. First, we Sanger sequenced many SNPs to select a highly false positive discriminating bioinformatics filter set, dropping from 20% to less than 1% false positive rate. We also selected some genes depending their significance (SPG11, SRCAP, AIM1L, FUS, TAF15, APOE ε status) to be Sanger sequenced to confirm the variants identified using the MiSeq. Finally the few SNPs identified with a coverage between 5 and 10x where also verified by Sanger sequencing. FastQ reads were aligned to the human reference genome (UCSC hg19, GRCh37, Feb. 2009 release) using bowtie2 [145] and SAMtools [146]. We applied GATK [147], [148] base quality score recalibration, indel realignment, duplicate removal, and performed coverage calculations, SNP and INDEL discovery and genotyping across each sample using optimized custom hard filtering parameters or variant quality score recalibration (raw variants were filtered using the following parameters: DP<5. 0, QUAL<30. 0, QD<2. 0, FS>50. 0, HaplotypeScore>13. 0, MQ<30. 0, MQRankSum <−12. 5, ReadPosRankSum <−8. 0). Variants were filtered against dbSNPv137,1000 genomes and ESP 6500 databases and were then annotated using ANNOVAR [149]. Fisher' s Exact tests were performed to determine if there were any enrichments among genes or categories of genes using the exact2×2 package [150] in the statistical programming tool R (version 3. 1. 1). We used a modified version of the method previously described [28]. However, since rare and novel variants are not in linkage disequilibrium (LD) with one another, we did not weight each variant by LD but by polyphen-2 score. For testing the distribution of deleterious variation score between cases and controls, we counted the number of individuals with a score ≥0. 85 (the cutoff for “probably damaging” in polyphen-2 [151], Table S8). Novel variants were determined to be those that were not present in either dbSNPv137, ESP6500 or 1000 genomes databases. Rare variants were determined to be those that were present at a frequency of less than or equal to 0. 000538 in the ESP6500 database. This value was chosen as it is the frequency which the ALS causative known SOD1 variant, p. D91A, is present in this database; we identified this variant in two patients. This subset also included variants which were present in dbSNPv137 at a very low or with no frequency listed, but were not present in ESP6500 and either not present or present at less than 0. 01 in the 1000 genomes database. Score and phenotypic impact predictions, when available, are provided for each variant using various algorithms. For each, a higher score indicates that a variant is predicted to be more deleterious. Algorithms used are PhyloP [152] (C: conserved, N: not conserved); SIFT [153] (D: deleterious, T: tolerated); PolyPhen2 [154] (D: probably damaging, P: possibly damaging, B: benign); MutationTaster [155] (A: disease causing automatic, D: disease causing, N: polymorphism, P: polymorphism automatic). N2A cells were plated on top of cover slides in 24-well format and transfected with Lipofectamine 2000 (Invitrogen) according to the manufacturer' s instructions. Cells were fixed in 4% PFA 24 h post-transfection and immunostained using primary anti-V5 mouse monoclonal antibody (R960-25 Invitrogen) and secondary Alexa Fluor 488 goat anti-mouse IgG antibody (A-11001 Invitrogen). Cells were mounted on microscope slides using ProLong Diamond antifade with DAPI (P36962 Invitrogen) and imaged using a Leica DMI600B microscope.
summary: Amyotrophic lateral sclerosis (ALS), also known as Charcot disease or Lou Gehrig' s disease, is one of the most common neuromuscular diseases worldwide. This disease is characterized by a progressive degeneration of motor neurons, leading to patient death within a few years after onset. Despite the fact that most ALS cases are sporadic, most of the ALS genetic studies have focused on familial forms, leading to the genetic determination of cause for 70% of cases of familial ALS but for only 10% of sporadic ALS cases. This, coupled with the dearth of families available for study, suggests that researchers should begin tapping into the relatively untouched reservoir of available sporadic samples to identify novel genetic causes of sporadic ALS. Here we take advantage of high-throughput target sequencing techniques to test four different hypotheses about the genetic causes of ALS in sporadic ALS and uncover new candidate genes and pathways implicated in ALS.
keywords: genetic dominance
  genetic disorders
  human genomics
  alleles
  gene function
  mutation
  genome analysis
  trait locus analysis
  genome annotation
  molecular genetics
  frameshift mutation
  autosomal dominant diseases
  missense mutation
  molecular biology
  genetic loci
  point mutation
  genetics
  biology and life sciences
  genomics
  genetics of disease
  computational biology
title: Targeted Exon Capture and Sequencing in Sporadic Amyotrophic Lateral Sclerosis